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9107 lines
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<td VALIGN=BOTTOM WIDTH="460" class="H1">NCBI Resource Guide</td>
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<!-- ============= PAGE_STRUCTURE ==================
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HORIZONTAL_NAVIGATION_BAR
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RIGHT_SIDE_OF_TABLE
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LEGEND_TABLE
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ABOUT_NCBI
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WhatsNew
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NCBINews
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OrganizationalStructure
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GENBANK OVERVIEW
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GENBANK SUBMISSIONS
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SPECIAL SUBMISSIONS TO GENBANK
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OTHER (NON-GENBANK) TYPES OF DATA SUBMISSIONS
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COLLABORATION
|
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FTP GENBANK
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MOLECULAR DATABASES
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MOLECULAR DATABASES: NUCLEOTIDES
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MOLECULAR DATABASES: PROTEINS
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MOLECULAR DATABASES: STRUCTURES
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MOLECULAR DATABASES: GENES
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MOLECULAR DATABASES: EXPRESSION
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MOLECULAR DATABASES: TAXONOMY
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LITERATURE
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GENOMES_AND_MAPS
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: BLAST
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: CLONES
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: MAPS
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: MAPPED MARKERS
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: CYTOGENETICS
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: GENE EXPRESSION
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: GENETIC VARIATION
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: DISORDERS
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: CANCER RESEARCH
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: FTP
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: MOUSE
|
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MOUSE GENOME SUB-CATEGORY: GUIDE
|
||
MOUSE GENOME SUB-CATEGORY: CHROMOSOMES
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||
MOUSE GENOME SUB-CATEGORY: SEQUENCES
|
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MOUSE GENOME SUB-CATEGORY: GENES
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||
MOUSE GENOME SUB-CATEGORY: CLONES
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MOUSE GENOME SUB-CATEGORY: MAPS
|
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MOUSE GENOME SUB-CATEGORY: CYTOGENETICS
|
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MOUSE GENOME SUB-CATEGORY: BLAST
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MOUSE GENOME SUB-CATEGORY: FTP
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: RAT
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: COW
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: ZEBRAFISH
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: DROSOPHILA
|
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: NEMATODE
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: PLANTS
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: YEAST
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: MALARIA
|
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: MICROBIAL GENOMES
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: VIRUSES
|
||
: VIROIDS
|
||
: PLASMIDS
|
||
: EUKARYOTIC_ORGANELLES
|
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TOOLS
|
||
: TEXT SEARCHING
|
||
: SEQUENCE SIMILARITY SEARCHING
|
||
: NUCLEOTIDE SEQUENCE ANALYSIS
|
||
: PROTEIN SEQUENCE ANALYSIS
|
||
: 3-D STRUCTURE DISPLAY AND SIMILARITY SEARCHING
|
||
: GENOME ANALYSIS
|
||
: GENE EXPRESSION
|
||
RESEARCH
|
||
SOFTWARE ENGINEERING
|
||
EDUCATION
|
||
: NEWS
|
||
: BOOKS
|
||
: GLOSSARIES
|
||
: TUTORIALS
|
||
: COURSES
|
||
: ADDITIONAL RESOURCES
|
||
FTP_SITE
|
||
CATEGORY WITHIN FTP_SITE: DATABASES
|
||
CATEGORY WITHIN FTP_SITE: GENOMES
|
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HUMAN_GENOME_PROJECT_FTP_DATA
|
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OTHER_GENOMES_FTP_DATA
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||
CATEGORY WITHIN FTP_SITE: SOFTWARE
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Revised
|
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<table CLASS="BAR" border="0" width="100%" cellspacing="0" cellpadding="3"
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bgcolor="#003366">
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<tr CLASS="BAR" align="CENTER">
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<td width="16%"><a href="/entrez/" class="BAR">PubMed</a></td>
|
||
<td width="16%"><a href="/Entrez/" class="BAR">Entrez</a></td>
|
||
<td width="16%"><a href="/BLAST/" class="BAR">BLAST</a></td>
|
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<td width="16%"><a href="/entrez/query.fcgi?db=OMIM"
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||
class="BAR">OMIM</a></td>
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<td width="16%"><a href="/Taxonomy/taxonomyhome.html"
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class="BAR">Taxonomy</a></td>
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<td width="16%"><a href="/Structure/" class="BAR">Structure</a></td>
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</tr>
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</table>
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<!-- ======================= the contents ========================== -->
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<!-- ================ INTRODUCTORY_NOTE ================= -->
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<p>
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<table BGCOLOR="#FFFFFF" BORDER="0" CELLSPACING=0 CELLPADDING=3 WIDTH="100%">
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<tr>
|
||
<td align="center" class="TEXT2">
|
||
<i>Each link in this <b>Resource Guide</b> leads to a <b>brief description of
|
||
the
|
||
resource</b> on this page, then to the resource itself. A graphical <a
|
||
href="index.html"><b><FONT color="CD5555">Site Map</FONT></b></a> and an <a
|
||
href="AlphaList.html"><b><FONT color="CD5555">Alphabetical Quicklinks
|
||
Table</FONT></b></a> provide direct links to resources and bypass the
|
||
descriptions.</i>
|
||
</td>
|
||
</tr>
|
||
</table>
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||
</p>
|
||
|
||
|
||
<!-- OLD TEXT: Each link in this <b>Resource Guide</b> leads to a <b>brief
|
||
description of the resource</b> on this page, then to the resource itself. This
|
||
guide allows browsing either by category or by an alphabetical listing.
|
||
Separate
|
||
files provide a graphical <a href="index.html"><b><FONT color="CD5555">Site
|
||
Map</FONT></b></a> and an <a href="AlphaList.html"><b><FONT
|
||
color="CD5555">Alphabetical Quicklinks Table</FONT></b></a>, which have
|
||
<b>direct
|
||
links</b> to resources and bypasses the descriptions -->
|
||
|
||
<!-- ===========TABLE_OF_CONTENTS_AND_ALPHA_TABLE============== -->
|
||
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||
<table WIDTH="100%" BORDER="0" CELLSPACING=0 CELLPADDING=0>
|
||
|
||
<!-- ============== LEFT_SIDE_OF_TABLE================ -->
|
||
|
||
<tr>
|
||
<td WIDTH="40%" BGCOLOR="#FFFFFF" valign="top">
|
||
<img SRC="spacer10.GIF" height="3" width="10" border=0><BR>
|
||
|
||
<table WIDTH="100%" BGCOLOR="#FFFFFF" BORDER="0" CELLSPACING=0 CELLPADDING=0>
|
||
|
||
<tr><td BGCOLOR="#e0eee0" CLASS="H2">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<img SRC="spacer10.GIF" height="5" width="5" border=0>
|
||
RESOURCES BY CATEGORY<BR>
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="7" width="10" border=0><BR>
|
||
<b><a href="#AboutNCBI">About NCBI</a></b></td>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#Programs">programs and services</a>,
|
||
<a href="#Contact">contact information</a>,
|
||
<a href="#NCBIHandbook">NCBI handbook</a>,
|
||
<a href="#News"><b>news</b></a> (<a href="#WhatsNew">what's new</a>, <a
|
||
href="#NCBINews">NCBI News</a>, <a href="#EmailLists">announcements
|
||
e-mail lists</a>, <a href="#RSSfeeds">RSS feeds</a>),
|
||
<a href="#ExhibitSchedule">exhibit schedule</a>,
|
||
<a href="#Fellows">postdoctoral fellowships</a>,
|
||
<a href="#OrganizationalStructure">organizational structure</a>,
|
||
<a href="#Statistics">resource statistics</a>,
|
||
<a href="#SiteSearch">site search</a></td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#GenBank">GenBank</a></b></td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#Overview">overview</a>, <a href="#Submissions">submit
|
||
sequences</a>, <a href="#SubmitGenomes">submit genomes</a>, <a
|
||
href="#SampleRecord">sample record</a>, <a href="#GenBankDivisions">GenBank
|
||
divisions</a>, <a href="#GenBankStatistics">statistics</a>, <a
|
||
href="#GenBankReleaseNotes">release notes</a>, <a
|
||
href="#Collaboration">international collaboration</a>, <a href="#FTPGenBank">FTP
|
||
GenBank</a></td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#Databases">Molecular Databases</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#Nucleotides">nucleotides</a>, <a
|
||
href="#Proteins">proteins</a>, <a href="#Structures">structures</a>, <a
|
||
href="#Genes">genes</a>, <a href="#Expression">gene expression</a>, <a
|
||
href="#Taxonomy">taxonomy</a>
|
||
</td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#Literature">Literature Databases</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#PubMed">PubMed</a>, <a
|
||
href="#PubMedCentral">PubMedCentral</a>, <a href="#Journals">Journals</a>, <a
|
||
href="#OMIM">OMIM</a>, <a href="#Books">Books</a>, <a
|
||
href="#CitationMatcher">Citation Matcher</a>
|
||
</td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#Genomes">Genomes and Maps</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote>
|
||
<a href="#MultipleOrganisms">organism collections</a> (including
|
||
<a href="#EntrezGenome">Entrez Genome</a>,
|
||
<a href="#EntrezGenomeProject">Entrez Genome Project</a>,
|
||
<a href="#MapViewer">Map Viewer</a>,
|
||
<a href="#GenomesEntrezGene">Entrez Gene</a>,
|
||
<a href="#GenomesUniGene">UniGene</a>,
|
||
<a href="#GenomesHomoloGene">HomoloGene</a>, and
|
||
<a href="#COGs">COGs</a>), and organism-specific resources, such as:
|
||
<a href="#HumanGenome">human</a>,
|
||
<a href="#MouseGenome">mouse</a>,
|
||
<a href="#RatGenome">rat</a>,
|
||
<a href="#CowGenome">cow</a>,
|
||
<a href="#ZebrafishGenome">zebrafish</a>,
|
||
<a href="#DrosophilaGenome"><i>Drosophila</i></a>,
|
||
<a href="#NematodeGenome">nematode</a>,
|
||
<a href="#PlantGenomes">plant genomes</a>,
|
||
<a href="#YeastGenome">yeast</a>,
|
||
<a href="#MalariaGenome">malaria</a>,
|
||
<a href="#MicrobialGenomes">microbial genomes</a>,
|
||
<a href="#ViralGenomes">viruses</a>,
|
||
<a href="#ViroidGenomes">viroids</a>,
|
||
<a href="#Plasmids">plasmids</a>,
|
||
<a href="#EukaryoticOrganelles">eukaryotic organelles</a>
|
||
</td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#Tools">Tools</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#Entrez">Entrez</a>, <a href="#LinkOut">LinkOut</a>,
|
||
<a href="#MyNCBI">My NCBI</a>, <a href="#BLAST">BLAST</a>,
|
||
<a href="#NucleotideSequenceAnalysis">nucleotide sequence analysis</a>,
|
||
<a href="#ProteinSequenceAnalysis">protein sequence analysis</a>,
|
||
<a href="#StructureTools">3-D structure display and similarity searching</a>,
|
||
<a href="#GenomeAnalysisTools">genome analysis</a>,
|
||
<a href="#GeneExpressionTools">gene expression</a>
|
||
</td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#Research">Research at NCBI</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#CBB">Computational Biology Branch (CBB)</a>, <a
|
||
href="#SeniorInvestigatorsInPubMed">senior investigators in PubMed</a>, <a
|
||
href="#SeminarSchedule">seminar schedule</a>, <a
|
||
href="#PostdoctoralFellows">postdoctoral fellowships</a>
|
||
</td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#SoftwareEngineering">Software Engineering</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#IEB">IEB home page</a>, <a href="#ToolBox">NCBI
|
||
ToolBox</a>,
|
||
<a href="#IEB_Research">R&D projects</a>, <a href="#ASN.1">ASN.1</a>
|
||
</td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#Education">Education</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote>
|
||
<a href="#News">news</a>,
|
||
<a href="#SciencePrimer">science primer</a>,
|
||
<a href="#EducationBooks">books</a>,
|
||
<a href="#Glossaries">glossaries</a>,
|
||
<a href="#Tutorials">tutorials</a>,
|
||
<a href="#Courses">courses</a>,
|
||
<a href="#AdditionalResources">additional resources</a>
|
||
</td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" class="H3">
|
||
<img SRC="spacer10.GIF" height="5" width="10" border=0><BR>
|
||
<b><a href="#FTPSite">FTP Site</a></b><td></tr>
|
||
|
||
<tr><td BGCOLOR="#FFFFFF" CLASS="TEXT">
|
||
<blockquote><a href="#FTPDatabases">download databases</a>, <a
|
||
href="#FTP_Genomes">genomes</a>, and <a href="#FTPSoftware">software</a>, <a
|
||
href="#FTP_ToolBox">NCBI Software ToolBox</a>
|
||
</td></tr>
|
||
</table>
|
||
|
||
</td>
|
||
|
||
<!-- ============== END_LEFT_SIDE_OF_TABLE================ -->
|
||
|
||
<!-- ============== RIGHT_SIDE_OF_TABLE=================== -->
|
||
|
||
<td WIDTH="60%" BGCOLOR="#FFFFFF" valign="top">
|
||
|
||
<table WIDTH="100%" BGCOLOR="#FFFFFF" BORDER="0" CELLSPACING=3 CELLPADDING=4>
|
||
|
||
<!-- ================ ROW 0 (HEADER) ================ -->
|
||
|
||
<tr>
|
||
<td BGCOLOR="#e0eee0" COLSPAN="3" ALIGN="CENTER">
|
||
<FONT CLASS="H2"><b>ALPHABETICAL INDEX</b></FONT>
|
||
<br><FONT CLASS="TEXT2"><b>with links to resource descriptions</b></FONT>
|
||
<br><FONT CLASS="TEXT2"><i>(To bypass descriptions, use the <a
|
||
href="AlphaList.html"><FONT color="CD5555"><b>Alphabetical Quicklinks
|
||
Table</b></FONT></a>.)</i></FONT></td>
|
||
</tr>
|
||
|
||
<!-- ================ ROW 1 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#AboutNCBI">About NCBI</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#SampleRecord">GenBank sample record</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#PlantGenomes">Plant Genomes</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 2 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#EmailLists">Announcements</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Genes">Genes</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Proteins">Protein Sequences</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 3 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#ASN.1">ASN.1</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#GenesAndDisease">Genes and Disease</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#PubChem">PubChem</a><!-- img SRC="new.gif" height="12" width="31"
|
||
border=0 --></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 4 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#BankIt">BankIt</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Genomes">Genomes</a> (<a href="#EntrezGenome">data</a>, <a
|
||
href="#EntrezGenomeProject">projects</a>, <a
|
||
href="#SubmitGenomes">submissions</a>)</td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#PubMed">PubMed</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 5 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#BLAST">BLAST</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#GENSAT">GENSAT</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#PubMedCentral">PubMed Central</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 6 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#BLink">BLink</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#GEO">GEO</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#RefSeq">RefSeq</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 7 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Books">Books</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Glossaries">Glossaries</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Research">Research at NCBI</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 8 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#CancerChromosomes">Cancer Chromosomes</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#NCBIHandbook">Handbook</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#ViralGenomes">Retroviruses</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 9 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#CCDS">CCDS</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#HIVInteractions">HIV Interactions</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#SAGEmap">SAGEmap</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 10 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#CDART">CDART</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#HTG">HTGs</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#SciencePrimer">Science Primer</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 11 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#CDD">CDD</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#HomoloGene">HomoloGene</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#SeminarSchedule">Seminars</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 12 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#CGAP">CGAP</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#HumanGenome">Human Genome Resources</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Sequin">Sequin</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 13 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Clones">Clones</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#HumanMouseMap">Human-Mouse Homology Maps</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#ShortReadArchive">Short Read<br> Archive</a>
|
||
<img SRC="new.gif" height="12" width="31" border=0></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 14 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Cn3D">Cn3D</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Journals">Journals</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="/entrez/query.fcgi?db=ncbisearch">Site Search</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 15 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#CoffeeBreak">Coffee Break</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#LinkOut">LinkOut</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#SKY_CGH">SKY/M-FISH & CGH Database</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 16 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#COGs">COGs</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MalariaGenome">Malaria</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#SoftwareEngineering">Software Engineering</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 17 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#CBB">Computational Biology Branch</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MapViewer">Map Viewer</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Splign">Splign</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 18 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Submissions">Data Submissions</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MeSH">MeSH</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Statistics">Statistics</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 19 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#dbEST">dbEST</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MGC">MGC</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Structures">Structures</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 20 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#dbGSS">dbGSS</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MicrobialGenomes">Microbial Genomes</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Submissions">Submit Data</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 21 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#dbMHC">dbMHC</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MMDB">MMDB</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Taxonomy">Taxonomy</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 22 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#dbSNP">dbSNP</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#ModelMaker">Model Maker</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Tools">Tools</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 23 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#dbSTS">dbSTS</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MutationDatabases">Mutation Databases</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#TPA">TPA</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 24 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Education">Education</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#MyNCBI">My NCBI</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#TraceArchive">Trace Archives</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 25 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#ePCR">e-PCR</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="http://www.ncbi.nlm.nih.gov/">NCBI Home</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#UniGene">UniGene</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 26 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Entrez">Entrez</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#NCBINews">NCBI News</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#UniSTS">UniSTS</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 27 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#EntrezUtilities">Entrez Utilities</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Nucleotides">Nucleotide Sequences</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#VAST">VAST</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 28 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#Expression">Expression</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#OMIM">OMIM</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#VecScreen">VecScreen</a></td>
|
||
|
||
</tr>
|
||
|
||
|
||
<!-- ================ ROW 29 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#FTPSite">FTP</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#OMSSA">OMSSA</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#ViralGenomes">Viruses</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 30 ================ -->
|
||
|
||
<tr>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#GenBank">GenBank</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#ORFFinder">ORF Finder</a></td>
|
||
|
||
<td WIDTH="33%" BGCOLOR="#e0eeee" CLASS="TEXT">
|
||
<a href="#WGS">WGS</a></td>
|
||
|
||
</tr>
|
||
|
||
<!-- ================ ROW 31 (SPACER ROW) ================ -->
|
||
|
||
<!-- tr>
|
||
<td BGCOLOR="#FFFFFF" COLSPAN="3" ALIGN="CENTER">
|
||
<IMG SRC="spacer10.GIF" width="15" height=1 border=0>
|
||
</td>
|
||
</tr -->
|
||
|
||
<!-- tr>
|
||
<td BGCOLOR="#FFFFFF" COLSPAN="3" ALIGN="CENTER">
|
||
<FONT size="2" color="0033CC"><i>Questions about NCBI resources to</i> <a
|
||
href="mailto:info@ncbi.nlm.nih.gov">info@ncbi.nlm.nih.gov</a></FONT><br>
|
||
<FONT size="2" color="0033CC"><i>Comments about site map to Renata Geer</i> <a
|
||
href="mailto:renata@ncbi.nlm.nih.gov">renata@ncbi.nlm.nih.gov</a></FONT></td>
|
||
</tr -->
|
||
|
||
</table>
|
||
</td></tr>
|
||
|
||
<!-- ============== END_RIGHT_SIDE_OF_TABLE=============== -->
|
||
|
||
</table>
|
||
<p></p>
|
||
<!-- =======END_TABLE_OF_CONTENTS_AND_ALPHA_TABLE================ -->
|
||
|
||
<!-- ================= "NEW" STARBURST LEGEND ===================== -->
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="10%" BGCOLOR="#FFFFFF"> </td>
|
||
<td WIDTH="80%" BGCOLOR="#FFFFFF" ALIGN="center" CLASS="TEXT2"><img
|
||
SRC="new.gif"
|
||
height="12" width="31" border=0> <FONT size="-1"><i>indicates a resource
|
||
which
|
||
has become available in the last 12 months.</i></FONT></td>
|
||
<td WIDTH="10%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
<!-- =============== END "NEW" STARBURST LEGEND ==================== -->
|
||
|
||
<!-- ==========================ABOUT_NCBI========================== -->
|
||
<a NAME="AboutNCBI"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" class="H3a">About NCBI</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a
|
||
href="/About/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/">About NCBI</a> - The science behind our
|
||
resources. An introduction for researchers, educators and the public. Includes
|
||
a <a
|
||
href="/About/primer/index.html">Science Primer</a>, with plain language
|
||
introductions to bioinformatics, genome mapping, molecular modeling, SNPs, ESTs,
|
||
microarray technology, molecular genetics, pharmacogenomics, and
|
||
phylogenetics.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Programs"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/glance/programs.html">Programs and Services</a>
|
||
-
|
||
basic research, databases and software, outreach and education</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Contact"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/glance/contact_info.html">Contact
|
||
Information</a> -
|
||
postal address, phone, e-mail addresses for various services</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="ExhibitSchedule"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/outreach/exhibitsched.html">Exhibit
|
||
Schedule</a> -
|
||
NCBI exhibits at upcoming conferences</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="NCBIHandbook"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook.TOC&depth=2">NCBI
|
||
Handbook</a> - an online book, written by NCBI staff, that discusses
|
||
the many resources available at NCBI. Each chapter is
|
||
devoted to one service; after a brief overview on using
|
||
the resource, there is an account of how the resource works,
|
||
including topics such as how data are included in a database,
|
||
database design, query processing, and how the different
|
||
resources relate to each other.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="OrganizationalStructure"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/glance/organizational.html">Organizational
|
||
Structure</a> - functions of the three NCBI branches: Computational Biology
|
||
Branch
|
||
(CBB), Information Engineering Branch (IEB), and Information Resources Branch
|
||
(IRB)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/glance/science_counselors.html">Board of
|
||
Scientific
|
||
Counselors</a> - advises the NIH Director and the Deputy Director for Intramural
|
||
Research; the NLM Director, and the NCBI Director about the intramural research
|
||
and
|
||
development programs of the NCBI.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
|
||
<a NAME="Fellows"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="Summary/postdoc.html">Postdoctoral Fellowships</a> -
|
||
general information, application procedure</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="Statistics"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="Summary/statistics.html">Statistics for NCBI
|
||
Resources</a>
|
||
-
|
||
A page listing statistics that are available for selected NCBI resources,
|
||
including
|
||
number of records present in various databases, number of genomes available at
|
||
NCBI
|
||
and statistics for the individual genomes, and server usage.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="SiteSearch"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=ncbisearch">Site Search</a> -
|
||
Search the NCBI web site and display results in various formats. The default
|
||
Homepage view sorts NCBI pages based on the number of other NCBI pages that link
|
||
to
|
||
them. The NCBI Site Search function is part of the Entrez system (described <a
|
||
href="#Entrez">below</a>). Therefore, the search features described in the <a
|
||
href="/bookshelf/br.fcgi?book=helpentrez&part=EntrezHelp">Entrez help document</a> also
|
||
apply to
|
||
the site search function.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="News"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">News and Announcements</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="WhatsNew"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/About/whatsnew.html">What's New</a> - recently
|
||
released
|
||
resources and enhancements to existing resources.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="NCBINews"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/bookshelf/br.fcgi?book=newsncbi">NCBI News</a> - announcements
|
||
about new resources, enhancements to existing resources, staff publications,
|
||
tutorials, FAQs.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="EmailLists"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="Summary/email_lists.html">NCBI Announcements Email
|
||
Lists</a> -
|
||
Receive announcements about changes and updates to a variety of NCBI services.
|
||
In
|
||
addition to a general NCBI-announce list, topic-specific e-mail lists are
|
||
available
|
||
for BLAST, GenBank, dbSNP, Genomes, LinkOut, RefSeq, Sequin, and Entrez
|
||
Utilities
|
||
(for making WWW Links to Entrez). Follow the link to the NCBI Announcements Email
|
||
Lists page to see a complete list of available topics. Information on <a
|
||
href="Summary/email_lists.html">how to subscribe</a> is provided.</li></ul>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="RSSfeeds"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/feed/">NCBI RSS Feeds</a> -
|
||
Receive announcements about various NCBI services using an RSS (Real simple syndication)
|
||
feed reader. RSS feeds are available for resources such as Bookshelf, HomoloGene,
|
||
PubMed Central, PubMed New and Noteworthy, Probe Database, and UniGene.
|
||
Follow the link to the NCBI RSS Feeds page to see a complete list of available topics.
|
||
Additional information about RSS is provided in a short series of
|
||
<a href="/feed/styles/help.html">FAQs</a>.</li></ul>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<!-- =======================END_ABOUT_NCBI========================== -->
|
||
|
||
<!-- =======================GENBANK=========================== -->
|
||
<a NAME="GenBank"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" class="H3a">GenBank</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a
|
||
href="/Genbank/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<table BORDER="0" WIDTH="98%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="95%" BGCOLOR="#FFFFFF">
|
||
<blockquote>
|
||
<a href="#Overview">General Information</a>
|
||
(<a href="#SampleRecord">sample record</a>,
|
||
<a href="#GenBankReleaseNotes">release notes</a>,
|
||
<a href="#GenBankDivisions">GenBank divisions</a>,
|
||
<a href="#GenBankStatistics">statistics</a>),
|
||
|
||
<a href="#Submissions">Submissions</a>
|
||
(<a href="#SpecialSubmissionsToGenBank">general</a>,
|
||
<a href="#GenBankReleaseNotes">special categories</a>,
|
||
<a href="#SubmittingOtherTypesOfData">other data types</a>),
|
||
|
||
<a href="#Collaboration">International Collaboration</a>,
|
||
<a href="#FTPGenBank">FTP GenBank</a>
|
||
</td>
|
||
<td CLASS="TEXT" WIDTH="5%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
<br>
|
||
|
||
<!-- ================GENBANK OVERVIEW================ -->
|
||
<a NAME="Overview"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">General Information</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<td CLASS="TEXT"><a href="/Genbank/index.html">What is GenBank?</a> - a
|
||
database of nucleotide sequences from >160,000 organisms. Records that are
|
||
annotated with coding region (CDS) features also include amino acid
|
||
translations.
|
||
GenBank belongs to an <b>international collaboration</b> of sequence databases
|
||
(described <a href="#Collaboration">below</a>), which also includes EMBL and
|
||
DDBJ.
|
||
GenBank is <b>updated daily</b> in NCBI search systems, and a <b>full
|
||
release</b> is issued on the FTP site approximately the 15th of every February,
|
||
April, June, August, October, and December. It contains all the data present in
|
||
GenBank as of the cutoff date specified in the <b>release notes</b> (described
|
||
<a
|
||
href="#GenBankReleaseNotes">below</a>). The FTP site also provides daily
|
||
cumulative
|
||
an non-cumulative update files (more about the FTP site <a
|
||
href="#FTP_GenBank">below</a>).</td>
|
||
</table>
|
||
|
||
<a NAME="SampleRecord"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="samplerecord.html">Sample Record</a> - detailed
|
||
description of each field in a GenBank record. <br>Includes, for example,
|
||
information about accession number formats, sequence identifiers (GI number and
|
||
accession.version), a listing of GenBank divisions, and more. Describes some
|
||
commonly annotated biological features, such as CDS, and provides links to
|
||
documents
|
||
that list and define the complete set of biological features that can be
|
||
annotated
|
||
on sequence records. Includes a link to a <a
|
||
href="/entrez/sutils/girevhist.cgi">sequence revision history tool</a> that can
|
||
be
|
||
used to track changes that have occurred to the sequence data in a record.
|
||
Also lists the Entrez search field(s) that can be used to search each part
|
||
of
|
||
a sequence record.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GenBankDivisions"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="samplerecord.html#GenBankDivisionB">GenBank
|
||
Divisions</a>
|
||
- summary of GenBank divisions, including abbreviations, full spellings,
|
||
information
|
||
about what the GenBank divisions are, and what they are <i>not</i>. (This
|
||
information is part of the GenBank sample record, described above.)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT">Access GenBank - through <a
|
||
href="/entrez/query.fcgi?db=Nucleotide">Entrez Nucleotides</a>. Search by
|
||
accession
|
||
number, author name, organism, gene/protein name, and a variety of other text
|
||
terms.
|
||
Additional information about Entrez is <a href="#Entrez">below</a>. Use <a
|
||
href="#BLAST">BLAST</a> for sequence similarity searches against GenBank and
|
||
other
|
||
databases. An option to download the GenBank full
|
||
release and updates via <a href="#FTPGenBank">FTP</a> is also available.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GenBankStatistics"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Genbank/genbankstats.html">Growth Statistics
|
||
(graph)</a>
|
||
- see also <a href="ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt">Release Notes</a>
|
||
sections 2.2.6 (per division statistics), 2.2.7 (per organism statistics), 2.2.8
|
||
(growth of GenBank). For statistics on other NCBI databases, please see the page
|
||
that summarizes sources of <a href="Summary/statistics.html">Statistics for NCBI
|
||
Resources</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GenBankReleaseNotes"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt">GenBank
|
||
Release
|
||
Notes</a> - A document that accompanies each full release (described in "<a
|
||
href="#Overview">What is GenBank?</a>", above) of the GenBank database. The release notes describe
|
||
the
|
||
format and content of the flat files that comprise the release. They also
|
||
include
|
||
notices of recent and upcoming changes, information about GenBank divisions,
|
||
growth
|
||
statistics, citing GenBank, and more.<b>
|
||
<UL>
|
||
<li><a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt">Current Release Notes</a></li>
|
||
<li><a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/release.notes/">Past Release Notes</a></li>
|
||
</UL>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Taxonomy/Utils/wprintgc.cgi?mode=c">Genetic
|
||
Codes</a> -
|
||
synopsis of 17 genetic codes; used to ensure correct translation of coding
|
||
sequences
|
||
in GenBank records.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GenBankBionetNewsgroup"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://www.bio.net/biomail/listinfo/genbankb/">GenBank Bionet
|
||
Newsgroup</a> - A moderated list that includes announcements of new GenBank releases, recent and upcoming changes, and discussion among subscribers. For information on how to subscribe by e-mail, see the <a href="Summary/email_lists.html">NCBI Announcements Email Lists</a> page.</td>
|
||
</tr>
|
||
</table>
|
||
<br>
|
||
|
||
<!-- ================GENBANK SUBMISSIONS================ -->
|
||
<a NAME="Submissions"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">GenBank Submissions</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">General Information</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Genbank/submit.html"><b>General information</b>
|
||
about
|
||
submitting nucleotide sequence data</a> to GenBank, receiving <a
|
||
href="/Genbank/submit.html#ref1"><b>accession numbers</b></a>, and making <a
|
||
href="/Genbank/submit.html#ref11"><b>updates</b> to records</a>. <a
|
||
href="#SpecialSubmissionsToGenBank"><b>Special types of submissions</b></a> to GenBank,
|
||
such as genomes, alignments, ESTs, GSSs, HTGs, STSs, and WGS are discussed
|
||
below.</li></ul>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td width="5%"> </td>
|
||
<td width="90%" BGCOLOR="#FFFFCC" CLASS="TEXT">
|
||
<blockquote><i><!-- FONT color="CD5555" -->In addition to GenBank, there are <a
|
||
href="#SubmittingOtherTypesOfData"><b>other databases at NCBI</b></a> to which a
|
||
variety of data types can be submitted
|
||
(<a href="#SubmitTPA">third party annotations (TPA)</a>,
|
||
<a href="#SubmitVariation">variation</a>,
|
||
<a href="#SubmitExpression">expression</a>,
|
||
<a href="#SubmitMHC">MHC data</a>,
|
||
<a href="#SubmitSKY_MFISH_CGH">SKY/M-FISH/CGH data</a>,
|
||
<a href="#SubmitTraceData">traces</a>).<!-- /FONT --></i></blockquote></li></ul>
|
||
|
||
<!-- blockquote>
|
||
Examples of other types of data include:
|
||
<ul>
|
||
<li><a href="#SubmitTPA"><i>Third Party Annotations (TPA) for GenBank
|
||
records</i></a></li>
|
||
<li><a href="#SubmitVariation"><i>Variation</i></a></li>
|
||
<li><a href="#SubmitExpression"><i>Expression</i></a></li>
|
||
<li><a href="#SubmitMHC"><i>Major Histocompatibility Complex (MHC)
|
||
data</i></a></li>
|
||
<li><a href="#SubmitSKY_MFISH_CGH"><i>Spectral Karyotyping (SKY), Multiple
|
||
Fluorescence In Situ Hybridization (M-FISH) and
|
||
Comparative Genomic Hybridization (CGH) data</i></a></li>
|
||
<li><a href="#SubmitTraceData"><i>Traces</i></a></i></li>
|
||
</ul>
|
||
</blockquote -->
|
||
|
||
</td>
|
||
<td width="5%"> </td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Submission Software Programs</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="BankIt"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/BankIt/">BankIt</a> - WWW submission tool for
|
||
one
|
||
or few submissions, designed to make the submission process quick and easy.
|
||
(BankIt also automatically uses <a href="#VecScreen">VecScreen</a> to
|
||
identify
|
||
segments of nucleic acid sequence which may be of vector, adapter, or linker
|
||
origin
|
||
to combat the problem of vector contamination in GenBank.)</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Sequin"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Sequin/">Sequin</a> - submission software
|
||
program
|
||
for one or many submissions, long sequences, complete genomes, alignments,
|
||
population/phylogenetic/mutation studies. Can be used as a stand-alone
|
||
application
|
||
or in a TCP/IP-based "network aware" mode, with links to other NCBI resources
|
||
and
|
||
software such as <a href="#Entrez">Entrez</a>. (Use <a
|
||
href="#VecScreen">VecScreen</a> prior to submission). To receive
|
||
announcements
|
||
about updates to the Sequin submission software, see the <a
|
||
href="Summary/email_lists.html">NCBI Announcements Email Lists</a>
|
||
page.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ===========SPECIAL SUBMISSIONS TO GENBANK=========== -->
|
||
|
||
<a NAME="SpecialSubmissionsToGenBank"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Special Types of Submissions to GenBank</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="95%" BGCOLOR="#FFFFFF" ALIGN="CENTER">
|
||
<a href="#SubmitGenomes">Genomes</a>,
|
||
<a href="#SubmitAlignments">Alignments</a>,
|
||
<a href="#SubmitESTs">ESTs</a>,
|
||
<a href="#SubmitGSSs">GSSs</a>,
|
||
<a href="#HTG">HTGs</a>,
|
||
<a href="#SubmitSTSs">STSs</a>,
|
||
<a href="#WGS">WGS</a> <br>
|
||
<!-- (<i><a href="#SubmittingOtherTypesOfData">See also submissions to other
|
||
(non-GenBank) databases</a>:
|
||
<a href="#SubmitTPA">TPA</a>,
|
||
<a href="#SubmitVariation">Variation</a>,
|
||
<a href="#SubmitExpression">Expression</a>,
|
||
<a href="#SubmitMHC">MHC</a>,
|
||
<a href="#SubmitSKY_MFISH_CGH">SKY, MFISH & CGH</a>,
|
||
<a href="#SubmitTraceData">Traces</a></i>) -->
|
||
</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitGenomes"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><b>Submission of complete genomes and other large
|
||
sequence
|
||
records</b> - Recent enhancements to Sequin make it convenient for genome
|
||
sequencing
|
||
centers to annotate their records with
|
||
Sequin and submit the resulting ASN.1 file to GenBank. After the Sequin files
|
||
are
|
||
prepared, large genomes should be submitted by ftp; write to
|
||
genomes@ncbi.nlm.nih.gov to
|
||
obtain an ftp account. Smaller records less than 350 kb can be sent by email to
|
||
gb-sub@ncbi.nlm.nih.gov. <br><br>
|
||
|
||
More information about submitting genomes and other large sequence records is
|
||
provided on the following pages: <a href="/Genbank/submit.html#ref6">GenBank
|
||
submissions</a>, <a href="/Sequin/">Sequin</a>, <a
|
||
href="/Sequin/table.html">tabular
|
||
layout for submitting annotated features</a>, <a
|
||
href="/Genbank/genomesubmit.html">bacterial genome submission
|
||
guidelines</a>.
|
||
<!-- old url is <a href="/genomes/static/instructions.html">bacterial genome submission
|
||
guidelines</a> --><br><br>
|
||
|
||
In addition, sequencing centers can register a sequencing project with NCBI
|
||
prior to
|
||
the submission of any data. This can be done through a <a
|
||
href="http://www.ncbi.nih.gov/genomes/mpfsubmission.cgi">Genome project
|
||
submission
|
||
form</a>. For each registered project, NCBI will create a sequencing project
|
||
page
|
||
that describes the project, links out to genome-specific reosurces, and provides
|
||
a
|
||
focal point for the addition of links to NCBI resources such as Map Viewer and
|
||
genomic BLAST. Projects can be listed publicly or remain unlisted, and
|
||
sequences
|
||
may be held until publication (the default), released immediately, or made
|
||
available
|
||
for BLAST searches only. The form can also be used to set up an FTP site for
|
||
the
|
||
upload of data to NCBI, or to specify a URL to be used by NCBI for download of
|
||
project or sequence data. (See Fall 2003/Winter 2004 issue of <a
|
||
href="http://www.ncbi.nlm.nih.gov/About/newsletter.html">NCBI News</a> for more
|
||
information.)</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitAlignments"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Genbank/submit.html#ref6">Alignments</a> -
|
||
submission of
|
||
aligned sequences from population, phylogenetic, or mutation studies. Several
|
||
sections of the <a href="/Sequin/sequin.hlp.html">Sequin Help Documentation</a>
|
||
also
|
||
include information on how to submit alignments, such as <a
|
||
href="/Sequin/sequin.hlp.html#SubmissionType">Submission Type</a>, <a
|
||
href="/Sequin/sequin.hlp.html#FASTA+GAPFormatforAlignedNucleotideSequences">FAST
|
||
A+GA
|
||
P Format for Aligned Nucleotide Sequences</a>, <a
|
||
href="/Sequin/sequin.hlp.html#PHYLIPFormatforAlignedNucleotideSequences">PHYLIP
|
||
Format for Aligned Nucleotide Sequences</a>, <a
|
||
href="/Sequin/sequin.hlp.html#NEXUSFormatforAlignedNucleotideSequences">NEXUS
|
||
Format
|
||
for Aligned Nucleotide Sequences</a>, <a
|
||
href="/Sequin/sequin.hlp.html#SourceModifiersforPHYLIPandNEXUS">Source Modifiers
|
||
for
|
||
PHYLIP and NEXUS</a>, <a
|
||
href="/Sequin/sequin.hlp.html#ImportingAlignedSetsofSegmentedSequences">Importin
|
||
g
|
||
Aligned Sets of Segmented Sequences</a>. Check the Sequin help documentation
|
||
for
|
||
other relevant sections. (See Fall 2003/Winter 2004 issue of <a
|
||
href="http://www.ncbi.nlm.nih.gov/About/newsletter.html">NCBI News</a> for an
|
||
example in the "Submissions Corner".)</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitESTs"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/dbEST/how_to_submit.html">ESTs</a> -
|
||
expressed
|
||
sequence tags; short, single pass read cDNA (mRNA) sequences. Also includes
|
||
cDNA
|
||
sequences from differential display experiments and RACE
|
||
experiments.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitGSSs"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/dbGSS/how_to_submit.html">GSSs</a> - genome
|
||
survey sequences; short, single pass read genomic sequences, exon trapped
|
||
sequences,
|
||
cosmid/BAC/YAC ends, others.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="HTG"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/HTGS/subinfo.html">HTGs</a> - high throughput
|
||
genome sequences from large scale genome sequencing centers; unfinished (phase
|
||
0, 1,
|
||
2) and finished (phase 3) sequences. (Note that contigs assembled from draft
|
||
and
|
||
finished human HTG sequences are accessible from the Map Viewer, described <a
|
||
href="#HumanChromosomeMapViews">below</a>.) <!-- and contigs assembled from
|
||
finished
|
||
mouse HTG sequences are accessible from the <a
|
||
href="#MouseGenomeSequencing">Mouse
|
||
Genome Sequencing</a> page.) --></li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitSTSs"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/dbSTS/how_to_submit.html">STSs</a> - sequence
|
||
tagged sites; short sequences that are operationally unique in the genome, used
|
||
to
|
||
generate mapping reagents.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="WGS"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Genbank/wgs.html">WGS</a> - data from Whole
|
||
Genome Shotgun <a href="/projects/WGS/WGSprojectlist.cgi">(WGS) sequencing
|
||
projects</a> can be submitted to GenBank. The data can
|
||
contain annotations and an entire project is updated as sequencing progresses.
|
||
WGS
|
||
submissions are given accession numbers in the format of four letters followed
|
||
by
|
||
eight digits, e.g., XXXX00000000. The four letters are a stable project_ID,
|
||
which
|
||
does not change as the project is updated. The first two digits represent the
|
||
version number, which corresponds to a particular project update. The last six
|
||
digits represent an individual contig within the WGS project. For example, if a
|
||
project's assigned accession number is XXXX00000000, then that project's first
|
||
assembly version would be XXXX01000000, and the first contig of that version
|
||
would
|
||
be XXXX01000001. (<a href="/Genbank/wgs.html">more...</a>)<br>
|
||
|
||
The nucleotide data from WGS projects go into the appropriate organismal <a
|
||
href="samplerecord.html#GenBankDivisionB">GenBank Divisions</a> and the BLAST
|
||
wgs
|
||
database. The protein translations of annotated coding sequences go into the
|
||
BLAST
|
||
protein nr database. In addition, quality data from many WGS projects are
|
||
submitted
|
||
to the <a href="/Traces/home/?cmd=show&foverview&m=main&s=overview">Trace Archives</a> (<a
|
||
href="#TraceArchive">described</a>
|
||
in the ResourceGuide section on <a href="#Nucleotides">Nucleotide Sequence
|
||
Databases</a>).
|
||
|
||
</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ===========OTHER (NON-GENBANK) TYPES OF DATA SUBMISSIONS=========== -->
|
||
|
||
<a NAME="SubmittingOtherTypesOfData"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Other Types of Data Submissions<br>
|
||
<FONT color="CD5555">(<b>Other NCBI databases, separate from GenBank, to which
|
||
data
|
||
can be submitted</b>)</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitTPA"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Genbank/tpa.html">Third Party Annotations
|
||
(TPA)</a> - a database of experimentally supported annotations on assemblies of
|
||
sequences already present in DDBJ/EMBL/GenBank. Whereas DDBJ/EMBL/GenBank
|
||
contains
|
||
primary sequence data and corresponding annotations submitted by the
|
||
laboratories
|
||
that did the sequencing, the TPA database contains third-party assemblies of
|
||
primary
|
||
data with experimentally supported annotation that has been published in a
|
||
peer-reviewed scientific journal. Details about how to submit data, as well as
|
||
examples of what can and cannot be submitted to TPA, are provided on the <a
|
||
href="/Genbank/tpa.html">TPA</a> home page. Additional information about the
|
||
TPA
|
||
database is provided <a href="#TPA">below</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitVariation"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/SNP/">Genetic Variation</a> - in humans and
|
||
other
|
||
organisms can be submitted to the <a href="/SNP/">NCBI Database of Single
|
||
Nucleotide
|
||
Polymorphisms (dbSNP)</a>. Although dbSNP is a separate database from
|
||
GenBank,
|
||
as noted above, SNP records include cross-references to GenBank records.
|
||
(<a
|
||
href="/SNP/get_html.cgi?whichHtml=how_to_submit"><b>submission
|
||
instructions</b></a>)
|
||
Additional information about dbSNP is <a
|
||
href="#dbSNP">below</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitExpression"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/geo/">Gene Expression</a> - data can be
|
||
submitted
|
||
to <a href="/geo/">Gene Expression Omnibus (GEO)</a> (<a
|
||
href="/geo/info/overview.html#deposit"><b>submission instructions</b></a>).
|
||
Additional information about GEO is <a
|
||
href="#GEO">below</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitMHC"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/mhc/">Major Histocompatibility Complex
|
||
(MHC)</a>
|
||
- DNA sequence and clinical data can be submitted to <a href="/mhc/">dbMHC</a>.
|
||
A <a
|
||
href="#dbMHC">brief description</a> of dbMHC is provided in the Molecular
|
||
Databases/Nucleotide Sequences section of this guide, and additional details are
|
||
available in the <a
|
||
href="/books/bv.fcgi?rid=handbook.chapter.ch11">NCBI
|
||
Handbook</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitSKY_MFISH_CGH"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/sky/">Spectral Karyotyping (SKY), Multiplex
|
||
Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic
|
||
Hybridization
|
||
(CGH)</a> - data can be submitted to the <a href="/sky/">NCI and NCBI SKY/M-FISH
|
||
&
|
||
CGH Database</a> (<a
|
||
href="http://www.ncbi.nlm.nih.gov/sky/ccap_helper.cgi?tsc=0"><b>submission instructions</b></a>) Additional information
|
||
about
|
||
the NCI and NCBI SKY/M-FISH & CGH Database is <a
|
||
href="#SKY_CGH">below</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SubmitTraceData"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Traces/home/?cmd=show&f=overview&m=main&s=overview">Trace Data</a> - can be
|
||
submitted to the <a href="/Traces/home/?cmd=show&f=overview&m=main&s=overview">Trace Archive</a>, a repository of
|
||
the
|
||
raw sequence traces generated by large sequencing projects. (<a
|
||
href="/Traces/trace.fcgi?cmd=show&f=rfc&m=main&s=rfc"><b>submission
|
||
instructions</b></a>) Additional information about the Trace Archives is
|
||
<a
|
||
href="#TraceArchive">below</a>.</li></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
<br>
|
||
|
||
<!-- ================COLLABORATION================ -->
|
||
<a NAME="Collaboration"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">International Nucleotide Sequence
|
||
Database Collaboration</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/projects/collab/">GenBank, DDBJ, EMBL</a> - Overview
|
||
of
|
||
collaborative projects and links to home pages. The GenBank, DDBJ (DNA Data
|
||
Bank of
|
||
Japan), and EMBL (European Molecular Biology Laboratory) databases share data on
|
||
a
|
||
daily basis and are therefore equivalent. The record formats and search systems
|
||
might differ among the databases, but the accession numbers, sequence data, and
|
||
annotations are the same in all of them. E.g., you can retrieve the record with
|
||
accession number U12345 from GenBank, DDBJ, or EMBL and it will contain the same
|
||
sequence data, references, etc. in all three databases.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/projects/collab/FT/index.html">DDBJ/EMBL/GenBank
|
||
Feature
|
||
Table</a> - feature table formats and standards used in the annotation of
|
||
sequence
|
||
records by the collaborating databases; makes possible sharing of data; includes
|
||
detailed appendices such as:
|
||
<li><a href="/projects/collab/FT/index.html#7.3">biological features reference
|
||
key</a> (<a href="/projects/collab/FT/index.html#7.3.2">alphabetical list</a>
|
||
also
|
||
available)</li>
|
||
<li><a href="/projects/collab/FT/index.html#7.4">feature qualifiers</a></li>
|
||
<li>IUPAC abbreviations for <a
|
||
href="/projects/collab/FT/index.html#7.5.1">nucleotides</a></li>
|
||
<li>IUPAC abbreviations for <a href="/projects/collab/FT/index.html#7.5.3">amino
|
||
acids</a></td></li>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ================FTP GENBANK================ -->
|
||
<a NAME="FTPGenBank"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">FTP GenBank and Daily Updates</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/genbank/">GenBank flat file
|
||
format</a> - see <a href="samplerecord.html">sample GenBank record</a> and
|
||
detailed
|
||
description in <a href=ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt>GenBank release
|
||
notes</a>; download most recent full release (described <a
|
||
href="#Overview">above</a>) and daily cumulative or non-cumulative update
|
||
files.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ASN1"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/ncbi-asn1/">ASN.1 format</a> -
|
||
Abstract Syntax Notation 1, an International Standards Organization (ISO) data
|
||
representation format; download most recent full release (described <a
|
||
href="#Overview">above</a>) and daily cumulative or non-cumulative update files.
|
||
(<a href="Summary/asn1.html">more on ASN.1</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="FASTA"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/blast/db/">FASTA format</a> -
|
||
definition line followed by sequence data only (<a
|
||
href="/BLAST/fasta.html">example</a>); see <a
|
||
href="ftp://ftp.ncbi.nih.gov/blast/db/README">readme</a> file for database
|
||
descriptions, including <b>nt.Z</b> (daily updated non-redundant BLAST
|
||
nucleotide
|
||
database, contains GenBank+EMBL+DDBJ+PDB sequences, but no EST, STS, GSS, or
|
||
HTGS
|
||
sequences), <b>nr.Z</b> (daily updated non-redundant proteins), <b>est.Z</b>,
|
||
<b>gss.Z</b>, <b>htg.Z</b>, <b>sts.Z</b>, and others.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
<br>
|
||
|
||
<!-- ======================END_ABOUT_GENBANK======================== -->
|
||
|
||
<!-- ====================MOLECULAR DATABASES========================== -->
|
||
<a NAME="Databases"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" class="H3a">Molecular Databases</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a
|
||
href="/Database/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<table BORDER="0" WIDTH="98%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="95%" BGCOLOR="#FFFFFF">
|
||
<blockquote>
|
||
<a href="#Nucleotides">Nucleotide Sequences</a>,
|
||
<a href="#Proteins">Protein Sequences</a>,
|
||
<a href="#Structures">Structures</a>,
|
||
<a href="#Genes">Genes</a>,
|
||
<a href="#Expression">Expression</a>,
|
||
<a href="#Taxonomy">Taxonomy</a>
|
||
</td>
|
||
<td CLASS="TEXT" WIDTH="5%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
<br>
|
||
|
||
<!-- ================MOLECULAR DATABASES: NUCLEOTIDES================ -->
|
||
<a NAME="Nucleotides"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Nucleotide Sequence Databases</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<a NAME="EntrezNucleotides"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=Nucleotide">Entrez
|
||
Nucleotides</a> -
|
||
combines data from a number of source databases, including GenBank, RefSeq, TPA,
|
||
and
|
||
PDB. Data can be searched by accession number, author name, organism,
|
||
gene/protein
|
||
name, and a variety of other text terms. Additional information about Entrez <a
|
||
href="#Entrez">below</a>. For retrieval of large data sets, Batch Entrez
|
||
(described
|
||
<a href="#BatchEntrez">below</a>) is available.</td>
|
||
</tr>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Genbank/index.html">GenBank</a> - a database of
|
||
nucleotide
|
||
sequences from >160,000 organisms. Records that are annotated with coding region
|
||
(CDS) features also include amino acid translations. GenBank belongs to an
|
||
international collaboration of sequence databases (described <a
|
||
href="#Collaboration">above</a>), which also includes EMBL and DDBJ. A <a
|
||
href="samplerecord.html"><b>sample record</b></a>, which provides a detailed
|
||
description of each field in a GenBank record, is also available. A variety of
|
||
sequence records exist in GenBank, such as characterized genes that have been
|
||
well-studied and annotated, batch produced sequences (ESTs, GSSs, STSs), high
|
||
throughput genomic sequences, complete genomes, and more. Additional information
|
||
about GenBank is given in the <a href="#GenBank">GenBank Overview</a> section of
|
||
this guide.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="RefSeq"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/RefSeq/">RefSeq</a> - NCBI database of Reference
|
||
Sequences. Curated, non-redundant set including genomic DNA contigs, mRNAs and
|
||
proteins for known genes, mRNAs and proteins for gene models, and entire
|
||
chromosomes. Accession numbers have the format of two letters, an underscore
|
||
bar,
|
||
and six digits. Nucleotide sequence records have accessions: NT_123456,
|
||
NM_123456,
|
||
NC_123456, NG_123456, XM_123456, XR_123456 (more info about <a
|
||
href="/RefSeq/key.html#accessions">accession numbers</a> and <a
|
||
href="/RefSeq/key.html#query">access</a>). Additional details about RefSeq are
|
||
provided in the <a
|
||
href="/books/bv.fcgi?rid=handbook.chapter.ch18">NCBI
|
||
Handbook</a>, which is available online in the <a
|
||
href="/entrez/query.fcgi?db=Books">Entrez Books</a> database.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><blockquote><a href="/projects/CCDS/">Consensus CoDing Sequence
|
||
(CCDS) Database</a> - The CCDS project is a collaborative effort to identify a
|
||
core set of <b>human protein coding regions</b> that are consistently annotated
|
||
and of high quality. The long term goal is to support convergence towards a
|
||
standard set of gene annotations on the human genome. The collaborators include
|
||
the
|
||
|
||
<a href="http://www.ncbi.nlm.nih.gov/">National Center for Biotechnology
|
||
Information</a> (NCBI, <a href="http://www.ncbi.nlm.nih.gov/mapview/">Map
|
||
Viewer</a>),
|
||
|
||
<a href="http://www.ebi.ac.uk/">European Bioinformatics Institute</a> (EBI, </a>
|
||
<a href="http://www.ensembl.org/">Ensembl</a>),
|
||
|
||
<a href="http://www.cbse.ucsc.edu/">University of California, Santa Cruz</a>
|
||
(UCSC, <a href="http://genome.ucsc.edu/cgi-bin/hgGateway">Genome Browser</a>), and
|
||
|
||
<a href="http://www.sanger.ac.uk/">Wellcome Trust Sanger Institute</a> (WTSI, <a
|
||
href="http://vega.sanger.ac.uk/">Vega</a>).
|
||
|
||
They identify the position of protein-coding regions of genes that are (1)
|
||
annotated consistently on the human genome by all of the participating centers and
|
||
(2) supported by transcript evidence, use of canonical splice sites, and other
|
||
quality assurance measures. Additional information about the curation, process
|
||
flow, and quality testing is available on the CCDS web site.</blockquote></td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="TPA"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Genbank/TPA.html">Third Party Annotation (TPA)
|
||
database</a> - a database of experimentally supported annotations on assemblies
|
||
of
|
||
sequences already present in DDBJ/EMBL/GenBank. Whereas DDBJ/EMBL/GenBank
|
||
contains
|
||
primary sequence data and corresponding annotations submitted by the
|
||
laboratories
|
||
that did the sequencing, the TPA database contains third-party assemblies of
|
||
primary
|
||
data with experimentally supported annotation that has been published in a
|
||
peer-reviewed scientific journal. Details about how to submit data, as well as
|
||
examples of what can and cannot be submitted to TPA, are provided on the <a
|
||
href="/Genbank/tpa.html">TPA</a> home page.
|
||
|
||
<blockquote><i>Note:</i> Although TPA records are derived from
|
||
DDBJ/EMBL/GenBank, TPA is actually a <b>separate database</b>. Therefore, TPA
|
||
records are not present in the GenBank <b>FTP</b> files, but will be available
|
||
in
|
||
separate FTP files.<br><br>
|
||
|
||
The TPA database uses an <b>accession format</b> similar to GenBank records
|
||
(e.g.,
|
||
two letters followed by six digits) and is organized into similar
|
||
<b>divisions</b>.
|
||
(A list of <a href="samplerecord.html#GenBankDivisionB">GenBank divisions</a> is
|
||
given in the <a href="samplerecord.html">GenBank Sample Record</a>. Some
|
||
divisions,
|
||
such as EST, GSS, HTG and are present in GenBank but will not be present in
|
||
TPA.)<br><br>
|
||
|
||
TPA records can be <b>easily recognized</b> because the definition lines begin
|
||
with
|
||
the the letters "TPA", and they contain "Third Party Annotation; TPA" in the
|
||
Keywords field. This is illustrated in a <b>sample TPA record</b>, <a
|
||
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&ter
|
||
m=BK
|
||
000627[pacc]&doptcmdl=GenBank">BK000627</a>.<br><br>
|
||
|
||
TPA records can be <b>retrieved</b> from <a
|
||
href="/entrez/query.fcgi?db=Nucleotide">Entrez Nucleotides</a> (described <a
|
||
href="#EntrezNucleotides">above</a>). To only see data from TPA, use the
|
||
"Index"
|
||
mode to select "tpa" from the Properties search field, or simply add the command
|
||
<b>AND tpa[prop]</b> to your query.<br><br>
|
||
|
||
<!-- TPA records can be retrieved from <a
|
||
href="/entrez/query.fcgi?db=Nucleotide">Entrez Nucleotides</a> (described <a
|
||
href="#EntrezNucleotides">above</a>). To only see data from TPA, you can use
|
||
the
|
||
Limits option (select "Only from TPA"), or select "srcdb_tpa" in the Properties
|
||
search field, or simply add the command <b>AND srcdb_tpa[prop]</b> to your
|
||
query.<br><br -->
|
||
|
||
Details about how to <b>submit data</b>, as well as examples of what can and
|
||
cannot
|
||
be submitted to TPA, are provided on the <a href="/Genbank/TPA.html">TPA home
|
||
page</a>. An announcement and additional information about the TPA database is
|
||
provided in section 1.4.5, "Third-Party Annotation and Consensus Sequences
|
||
(TPA)" of
|
||
the <a href="ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt">GenBank 133.0 release
|
||
notes</a>.</blockquote>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="dbEST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/dbEST/index.html">dbEST</a> - database of expressed
|
||
sequence tags; short, single pass read cDNA (mRNA) sequences. Also includes
|
||
cDNA
|
||
sequences from differential display experiments and RACE experiments.<br>
|
||
<i>Note:</i> EST sequences are available from two sources: dbEST and the EST
|
||
division of GenBank. The sequences and accession numbers in both sources are the
|
||
same but the record formats differ. (<a
|
||
href="/dbEST/how_to_submit.html">data
|
||
submission instructions...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="dbGSS"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/dbGSS/index.html">dbGSS</a> - database of genome
|
||
survey
|
||
sequences; short, single pass read genomic sequences, exon trapped sequences,
|
||
cosmid/BAC/YAC ends, others.<br> <i>Note:</i> GSS sequences are available from
|
||
two
|
||
sources: dbGSS and the GSS division of GenBank. The sequences and accession
|
||
numbers
|
||
in both sources are the same but the record formats differ. (<a
|
||
href="/dbGSS/how_to_submit.html">data submission instructions...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="dbMHC"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mhc/">dbMHC</a> - Provides a platform where the human
|
||
leukocyte antigen (HLA) community can submit, edit, view, and exchange Major
|
||
Histocompatibility Complex (MHC) data. The MHC database is fully integrated with
|
||
other NCBI resources, as well as with the International Histocompatibility Working
|
||
Group (<a href="http://www.ihwg.org/">IHWG</a>) Web site, and provides links to
|
||
the IMmunoGeneTics HLA (<a href="http://www.ebi.ac.uk/imgt/hla/">IMGT/HLA</a>)
|
||
database. Additional details are available in the <a
|
||
href="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.1776">NCBI
|
||
Handbook</a>. <!-- Provides a
|
||
platform for genetic and clinical data related to the human Major
|
||
Histocompatibility Complex (MHC) where the human leukocyte antigen (HLA) community
|
||
can submit, edit, view, exchange, and analyze MHC data. -->
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="dbSNP"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/SNP/">dbSNP</a> - database of single nucleotide
|
||
polymorphisms, small-scale insertions/deletions, polymorphic repetitive
|
||
elements,
|
||
and microsatellite variation. dbSNP includes polymorphism data that is
|
||
experimentally derived, computationally derived, as well as hybrid data that is
|
||
determined by the alignment of an experimentally derived molecule to genomic
|
||
sequence data. Currently, dbSNP is comprised of 4 general classes of
|
||
submissions: (a) The SNP Consortium (TSC) - candidate SNPs identified by
|
||
sequencing
|
||
using either the reduced representation shotgun strategy or by alignment of
|
||
random
|
||
reads to genomic sequence; (b)
|
||
Overlaps - candidate SNPs were identified in sequence overlaps between
|
||
individual
|
||
BACs or PACs; (c) ESTs - SNPs identified in EST clusters, including those
|
||
identified by the Cancer Genome Anatomy Project (described <a
|
||
href="#CGAP">below</a>); (d) Other - SNPs identified after screening
|
||
larger
|
||
numbers of chromosomes include many with alleles of lower frequency (1%-20%).
|
||
(<a href="/SNP/get_html.cgi?whichHtml=how_to_submit">data submission
|
||
instructions</a>) To receive announcements about updates and new
|
||
features to dbSNP, see the <a href="Summary/email_lists.html">NCBI Announcements
|
||
Email Lists</a>
|
||
page.<br>
|
||
<i>Note:</i> Although dbSNP is a separate database from GenBank, SNP records
|
||
include
|
||
cross-references to GenBank records. </td>
|
||
</tr>
|
||
|
||
<a NAME="dbSTS"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/dbSTS/index.html">dbSTS</a> - database of sequence
|
||
tagged
|
||
sites; short sequences that are operationally unique in the genome, used to
|
||
generate
|
||
mapping reagents.<br> <i>Note:</i> STS sequences are available from two
|
||
sources:
|
||
dbSTS and the STS division of GenBank. The sequences and accession numbers in
|
||
both
|
||
sources are the same but the record formats differ. (<a
|
||
href="/dbSTS/how_to_submit.html">data submission instructions...</a>)</td></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="UniSTS"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/unists/">UniSTS</a> - a unified, non-redundant
|
||
view
|
||
of sequence tagged sites (STSs). UniSTS integrates marker and mapping data from
|
||
a
|
||
variety of public resources. If two or more markers have different names but
|
||
the
|
||
same primer pair, a single STS record is presented for the primer pair and all
|
||
the
|
||
marker names are shown. Each UniSTS record displays the primer sequences,
|
||
product
|
||
size, mapping information, and cross references to Entrez Gene, dbSNP, RHdb, GDB,
|
||
MGD,
|
||
and the Map Viewer. The marker report also lists GenBank and RefSeq records that
|
||
contain the primer sequences, as determined by <a href="#ePCR">Electronic PCR
|
||
(e-PCR)</a>. Data sources include dbSTS, RHdb, GDB, various human maps
|
||
(Genethon
|
||
genetic map, Marshfield genetic map, Whitehead RH map, Whitehead YAC map,
|
||
Stanford
|
||
RH map, NHGRI chr 7 physical map, WashU chrX physical map), various mouse maps
|
||
(Whitehead RH map, Whitehead YAC map, Jackson laboratory's MGD map).</td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3">Complete Genomes</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li>see the <a href="#Genomes">Genomes and Maps</a> section
|
||
below; includes resources for
|
||
<a href="#MultipleOrganisms">multiple organisms (<i>Entrez Genome</i>)</a>,
|
||
<a href="#HumanGenome">human</a>,
|
||
<a href="#MouseGenome">mouse</a>,
|
||
<a href="#RatGenome">rat</a>,
|
||
<a href="#ZebrafishGenome">zebrafish</a>,
|
||
<a href="#DrosophilaGenome"><i>Drosophila</i></a>,
|
||
<a href="#NematodeGenome">nematode</a>,
|
||
<a href="#PlantGenomes">plant genomes</a>,
|
||
<a href="#YeastGenome">yeast</a>,
|
||
<a href="#MalariaGenome">malaria</a>,
|
||
<a href="#MicrobialGenomes">microbial genomes</a>,
|
||
<a href="#ViralGenomes">viruses</a>,
|
||
<a href="#ViroidGenomes">viroids</a>,
|
||
<a href="#Plasmids">plasmids</a>,
|
||
<a href="#EukaryoticOrganelles">eukaryotic organelles</a>
|
||
</ul></td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/">UniGene</a> - ESTs and full-length mRNA
|
||
sequences organized into clusters that each represent a unique known or putative
|
||
gene within the organism from which the sequences were obtained. UniGene
|
||
clusters
|
||
are annotated with mapping and expression information when possible (e.g., for
|
||
human), and include cross-references to other resources. Sequence data can be
|
||
downloaded by cluster through the UniGene web pages, or the complete data set
|
||
can be
|
||
downloaded from the <a
|
||
href="ftp://ftp.ncbi.nih.gov/repository/UniGene/">repository/UniGene</a>
|
||
directory
|
||
of the FTP site. In addition, <b>UniGene DDD</b> (described <a
|
||
href="#UniGeneDDD">below</a>) can be used to show differential expression of
|
||
genes
|
||
between cDNA libraries. The <b>organisms represented</b> in UniGene are listed
|
||
on
|
||
the <a href="/UniGene/">UniGene home page</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/HomoloGene/">HomoloGene</a> - a gene homology tool
|
||
that
|
||
compares nucleotide sequences between pairs of organisms in order to identify
|
||
putative orthologs. Curated orthologs are incorporated from a variety of
|
||
sources
|
||
via Entrez Gene. Organisms represented are listed on the HomoloGene home
|
||
page.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://mgc.nci.nih.gov/">Mammalian Gene Collection
|
||
(MGC)</a> - The NIH Mammalian Gene Collection (MGC) is a trans-NIH initiative
|
||
that
|
||
seeks to identify and sequence a representative full open reading frame (FL-ORF)
|
||
clone for each human, mouse, and rat gene. The MGC project entails the
|
||
production
|
||
of cDNA libraries and sequences, database and repository development, as well as
|
||
the
|
||
support of research for improved library construction, sequencing, and analytic
|
||
technologies. All the resources generated by the MGC are publicly accessible to
|
||
the
|
||
biomedical research community.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="TraceArchive"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Traces/home/?cmd=show&f=overview&m=main&s=overview">Trace Archives</a> - a repository
|
||
of
|
||
the raw sequence traces generated by large sequencing projects. It allows
|
||
retrieval
|
||
of both the sequence file and the underlying data which generated the file. In
|
||
the
|
||
case of projects that rely on a Whole Genome Shotgun (WGS) strategy, the Trace
|
||
Archive will be the sole source of raw sequence data. (More information about
|
||
WGS projects
|
||
is provided in the ResourceGuide section on <a
|
||
href="#SpecialSubmissionsToGenBank">special
|
||
types of submissions to GenBank</a>/<a href="#WGS">WGS</a>.)
|
||
NCBI will be exchanging data regularly with the
|
||
<a href="http://trace.ensembl.org/">Ensembl Trace Server</a>.
|
||
The Trace Archive can be searched by using <a
|
||
href="http://blast.ncbi.nlm.nih.gov/BLAST.cgi?PAGE=Nucleotide&PROGRAM=blastn&BLAST_PROGRAMS=megaBLAST&PAGE_TYPE=BlastSearch">
|
||
Trace BLAST</a>
|
||
(described <a
|
||
href="#TraceBLAST">below</a>), or by entering a term in the search
|
||
box at
|
||
the top of the Trace Archives Page. (<a
|
||
href="/Traces/trace.fcgi?cmd=show&f=rfc&m=main&s=rfc">data submission
|
||
instructions...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ShortReadArchive"></a>
|
||
<table BORDER="0" CELLSPACING="5" width="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td class="text"><blockquote><a href="/Traces/sra/sra.cgi?cmd=show&f=main&m=main&s=main">Short Read Archive</a> -
|
||
houses sequencing data generated by new sequencing platforms.</blockquote></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><blockquote><a href="/Traces/assembly/assmbrowser.cgi">Assembly
|
||
Archive</a> - links the raw sequence information found in the
|
||
<a href="/Traces/home/">Trace Archives</a> with assembly information
|
||
found in publicly available sequence repositories (<a
|
||
href="/Genbank/index.html">GenBank/EMBL/DDBJ</a>).
|
||
The Assembly Viewer allows a user to see the multiple sequence alignments as
|
||
well as
|
||
the actual sequence chromatogram.</blockquote></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="UniVec"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/VecScreen/UniVec.html">UniVec</a> - a database that
|
||
can
|
||
be used to quickly identify segments within nucleic acid sequences which may be
|
||
of
|
||
vector origin. Screening using UniVec is efficient because a large number of
|
||
redundant sub-sequences have been eliminated to create a database that contains
|
||
only
|
||
one copy of every unique sequence segment from a large number of vectors. The
|
||
<b>VecScreen</b> tool, described <a href="#VecScreen">below</a> (under sequence
|
||
analysis tools), can be used to compare a query sequence against the UniVec
|
||
database
|
||
in order to identify possible <a href="/VecScreen/contam.html">vector
|
||
contamination</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT">Genomes - Resources in the <a href="#Genomes">Genomes and
|
||
Maps</a>
|
||
section contain the nucleotide sequences for a variety of genomes. Examples of
|
||
the
|
||
genomes available include:
|
||
<a href="#MultipleOrganisms">>1000 organisms in <i>Entrez Genome</i></a>,
|
||
<a href="#HumanGenome">human</a>,
|
||
<a href="#MouseGenome">mouse</a>,
|
||
<a href="#RatGenome">rat</a>,
|
||
<a href="#ZebrafishGenome">zebrafish</a>,
|
||
<a href="#DrosophilaGenome"><i>Drosophila</i></a>,
|
||
<a href="#NematodeGenome">nematode</a>,
|
||
<a href="#PlantGenomes">plant genomes</a>,
|
||
<a href="#YeastGenome">yeast</a>,
|
||
<a href="#MalariaGenome">malaria</a>,
|
||
<a href="#MicrobialGenomes">microbial genomes</a>,
|
||
<a href="#ViralGenomes">viruses</a>,
|
||
<a href="#ViroidGenomes">viroids</a>,
|
||
<a href="#Plasmids">plasmids</a>,
|
||
<a href="#EukaryoticOrganelles">eukaryotic organelles</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="#NucleotideSequenceAnalysis">Nucleotide Sequence
|
||
Analysis</a> - various tools are available for analyzing nucleotide sequences
|
||
and
|
||
are described <a href="#NucleotideSequenceAnalysis">below</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ================MOLECULAR DATABASES: PROTEINS================ -->
|
||
<a NAME="Proteins"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Protein Sequence Databases</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=Protein">Entrez Proteins</a> -
|
||
search protein sequence records (from GenPept + RefSeq + Swiss-Prot + PIR + RPF
|
||
+
|
||
PDB) by accession number, author name, organism, gene/protein name, and a
|
||
variety of
|
||
other text terms. Additional information about Entrez <a
|
||
href="#Entrez">below</a>.
|
||
For retrieval of large data sets, <b>Batch Entrez</b> (described <a
|
||
href="#BatchEntrez">below</a>) is available. Entrez proteins also includes
|
||
<b>BLink</b> ("BLAST Link"), a feature which displays the results of BLAST
|
||
searches
|
||
that have been done for every protein sequence in the Entrez Proteins data
|
||
domain.
|
||
To access it, follow the BLink link displayed beside any hit in the results of
|
||
an
|
||
Entrez Proteins search. More information about BLink is provided <a
|
||
href="#BLink">below</a>.</td>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/RefSeq/">RefSeq</a> - NCBI database of Reference
|
||
Sequences. Curated, non-redundant set including genomic DNA contigs, mRNAs and
|
||
proteins for known genes, mRNAs and proteins for gene models, and entire
|
||
chromosomes. Accession numbers have the format of two letters, an underscore
|
||
bar,
|
||
and six digits. Protein sequence records have accessions: NP_123456 or
|
||
XP_123456
|
||
(more info about <a href="/RefSeq/key.html#accessions">accession numbers</a> and
|
||
<a
|
||
href="/RefSeq/RSfaq.html#access">access</a>).</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/genbank/">FTP GenPept</a> -
|
||
download the "relxxx.fsa_aa.gz" file. The filename stands for "Release number
|
||
XXX
|
||
FASTA formatted amino acid translations". The translations are extracted from
|
||
GenBank/EMBL/DDBJ records that are annotated with one or more CDS features</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CDD"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/cdd/cdd.shtml">Conserved Domain Database
|
||
(CDD)</a> - a collection of
|
||
sequence alignments and profiles representing protein domains
|
||
conserved in molecular evolution. It includes domains
|
||
from <a href="http://smart.embl-heidelberg.de/">Smart</a> and
|
||
<a href="http://pfam.wustl.edu/">Pfam</a>, as well as domains
|
||
contributed by NCBI researchers. It also includes alignments
|
||
of the domains to known 3-dimensional protein structures in the
|
||
MMDB database (described <a href="#MMDB">below</a>).
|
||
CDD can be used to identify conserved domains in a protein query
|
||
sequence, using the <b>CD-Search</b> service (described
|
||
<a href="#CD-Search">below</a>). In addition, the <b>CDART</b> tool
|
||
(described <a href="#CDART">below</a>) uses CDD and RPS-BLAST (described <a
|
||
href="#RPS-BLAST">below</a>) to retrieve proteins with similar domain
|
||
architectures.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/RefSeq/HIVInteractions/">HIV Interactions</a> - The
|
||
HIV-1, Human Protein Interaction Database contains information about known
|
||
interactions of HIV-1 proteins with proteins from human hosts. It provides
|
||
annotated bibliograhies of published reports of protein interactions, with links
|
||
to
|
||
the corresponding PubMed records and sequence data. <a
|
||
href="#HIVInteractions">More
|
||
information</a> about this database is provided under "Literature Databases".
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PROW"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/prow/">PROW</a> - Protein Resources on the Web -
|
||
short
|
||
authoritative guides on the approximately 200 human CD cell-surface molecules.
|
||
Peer-reviewed; provides approximately 20 standardized categories of information
|
||
(biochemical function, ligands, etc.) for each CD antigen.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="#ProteinSequenceAnalysis">Protein Sequence
|
||
Analysis</a> -
|
||
various tools are available for analyzing protein sequences and are described <a
|
||
href="#ProteinSequenceAnalysis">below</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3">Proteomes</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li>Resources in the <a href="#Genomes">Genomes and
|
||
Maps</a>
|
||
section contain annotations for the proteins encoded by a variety of genomes.
|
||
Examples of the genomes available include:
|
||
<a href="#MultipleOrganisms">>1000 organisms in <i>Entrez Genome</i></a>,
|
||
<a href="#HumanGenome">human</a>,
|
||
<a href="#MouseGenome">mouse</a>,
|
||
<a href="#RatGenome">rat</a>,
|
||
<a href="#ZebrafishGenome">zebrafish</a>,
|
||
<a href="#DrosophilaGenome"><i>Drosophila</i></a>,
|
||
<a href="#NematodeGenome">nematode</a>,
|
||
<a href="#PlantGenomes">plant genomes</a>,
|
||
<a href="#YeastGenome">yeast</a>,
|
||
<a href="#MalariaGenome">malaria</a>,
|
||
<a href="#MicrobialGenomes">microbial genomes</a>,
|
||
<a href="#ViralGenomes">viruses</a>,
|
||
<a href="#ViroidGenomes">viroids</a>,
|
||
<a href="#Plasmids">plasmids</a>,
|
||
<a href="#EukaryoticOrganelles">eukaryotic organelles</a>.
|
||
|
||
The proteomes of human, mouse, rat, and a growing number of other eukaryotes are
|
||
also shown as annotations on the genomes of those organisms in <b>Map Viewer</b>
|
||
(<a
|
||
href="#MapViewer">described</a> in the <a href="#Genomes">Genomes and Maps</a>
|
||
section). MapViewer can display the data graphically or in tabular format, and
|
||
also
|
||
provides links to corresponding data on the FTP site.
|
||
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ProtTaxTable"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=Genome">Entrez
|
||
Genome</a> -
|
||
provides ProtTable and TaxTable for various organisms. The <b>ProtTable</b>
|
||
provides a summary of protein coding regions in a genome, and provides links to
|
||
the
|
||
corresponding nucleotide and protein sequences in FASTA format. The
|
||
<b>TaxTable</b>, also referred to as the "<b>distribution of BLAST protein
|
||
homologs
|
||
by taxa</b>," summarizes the results of BLAST analyses done for the proteins,
|
||
and
|
||
displays the relationship of the organism to others through a color-coded
|
||
graphical
|
||
summary. (Additional information about Entrez Genome is provided <a
|
||
href="#EntrezGenome">below</a>.)</ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/">FTP
|
||
Genome Proteins</a> - download an *.faa file (FASTA formatted amino acid
|
||
sequences)
|
||
and *ptt file (protein table) for various organisms from the genbank/genomes
|
||
directory of the ftp site; see <a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/genomes/README">readme</a> file for more
|
||
information. Protein tables can also be viewed in Entrez Genome, as noted
|
||
above.</li></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ================MOLECULAR DATABASES: STRUCTURES================ -->
|
||
<a NAME="Structures"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Structure Databases</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/">Structure Home</a> - general information
|
||
about the NCBI Structure Group and its research projects, as well as access to
|
||
the
|
||
Molecular Modeling Database (MMDB) and related tools to search and display
|
||
structures.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MMDB"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/MMDB/mmdb.shtml">MMDB: Molecular Modeling
|
||
Database</a>- a database of three-dimensional biomolecular structures derived
|
||
from
|
||
X-ray crystallography and NMR-spectroscopy. MMDB is a subset of
|
||
three-dimensional
|
||
structures obtained from the Brookhaven Protein DataBank (PDB), excluding
|
||
theoretical models. MMDB reorganizes and validates the information in a way
|
||
that
|
||
enables cross-referencing between the chemistry and the three-dimensional
|
||
structure
|
||
of macromolecules. Its data specification includes a description of a
|
||
biopolymer's
|
||
spatial structure, a description of how it is organized chemically, and a set of
|
||
pointers linking the two. By integrating chemical, sequence, and structure
|
||
information, MMDB is designed to serve as a resource for structure-based
|
||
homology
|
||
modeling and protein structure prediction. MMDB records are stored in <a
|
||
href="#ASN1">ASN.1</a> format and can be displayed with the <a
|
||
href="#Cn3D">Cn3D</a>, Rasmol, or Kinemage viewers. In addition, similar
|
||
structures
|
||
within the database have been identified using<a href="#VAST">VAST</a>, and new
|
||
structures can be compared against the database using <a
|
||
href="#VASTSearch">VASTsearch</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="3D_Domains"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=Domains">3D Domains Database</a>
|
||
-
|
||
compact structural domains identified automatically in MMDB, Entrez's
|
||
macromolecular
|
||
three-dimensional structure database. These domains are identified by searching
|
||
for
|
||
breakpoints in the structure between major secondary structure elements so that
|
||
the
|
||
ratio of intra- to inter-domain contacts falls above a set threshhold. 3D
|
||
Domains
|
||
are the units of comparison for structure neighbor ("related structures")
|
||
calculations using the VAST algorithm.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/cdd/cdd.shtml">Conserved Domain Database
|
||
(CDD)</a> - a collection of
|
||
sequence alignments and profiles representing protein domains
|
||
conserved in molecular evolution. It includes domains
|
||
from <a href="http://smart.embl-heidelberg.de/">Smart</a> and
|
||
<a href="http://pfam.wustl.edu/">Pfam</a>, as well as domains
|
||
contributed by NCBI researchers. It also includes alignments
|
||
of the domains to known 3-dimensional protein structures in the
|
||
MMDB database (described <a href="#MMDB">above</a>).
|
||
CDD can be used to identify conserved domains in a protein query
|
||
sequence, using the <b>CD-Search</b> service (described
|
||
<a href="#CD-Search">below</a>). In addition, the <b>CDART</b> tool
|
||
(described <a href="#CDART">below</a>) uses CDD and RPS-BLAST (described <a
|
||
href="#RPS-BLAST">below</a>) to retrieve proteins with similar domain
|
||
architectures.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PubChem"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://pubchem.ncbi.nlm.nih.gov/">PubChem</a> -
|
||
contains
|
||
the chemical structures of small organic molecules and information on their
|
||
biological activities.
|
||
It is intended to support the Molecular Libraries and Imaging component of the
|
||
<a
|
||
href="http://nihroadmap.nih.gov/">NIH Roadmap Initiative</a>.
|
||
PubChem's chemical structure database may be searched on the basis of
|
||
descriptive
|
||
terms, chemical properties, and structural similarity.
|
||
When possible, PubChem's chemical structure records are linked to other NCBI
|
||
databases, including the <a href="/entrez/query.fcgi?db=PubMed">PubMed</a>
|
||
scientific literature database and NCBI's <a
|
||
href="/entrez/query.fcgi?db=Structure">protein 3D structure database</a>.
|
||
PubChem also contains the results of high-throughput biological screening
|
||
experiments. PubChem is organized as three linked databases within the
|
||
<a href="/Entrez/">Entrez/PubMed</a> information retrieval system. <!--
|
||
Background
|
||
information about the project is provided in a summer 2004 article in the <a
|
||
href="http://www.nih.gov/catalyst/2004/04.05.01/page1a.html">NIH Catalyst</a>.
|
||
-->
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PubChemSubstance"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=pcsubstance">PubChem
|
||
Substance</a> - Primary data NCBI obtains from the various public depositories.
|
||
The PubChem Substance database contains approximately <!-- database statistic -->13 million
|
||
records as of October 2006, provided by various sources, DTP/NCI, NIAID, ChemIDplus,
|
||
NIST, NIST webbook, MOLI/NCI, ChemBank, MMDB, KEGG, and more.
|
||
Substance information includes chemical structures, synonyms,
|
||
registration IDs, descriptions, related urls, and database cross-reference links
|
||
to PubMed, protein 3D structures, and biological screening results.</li></ul></td>
|
||
<!-- OLD DESCRIPTION, THROUGH 10/18/06:
|
||
td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=pcsubstance">PubChem
|
||
Substance</a> - Primary data NCBI obtains from the various public depositories.
|
||
The substance database currently contains approximately <database statistic>18 million
|
||
records (as of October 2006) provided by various sources, DTP/NCI, NIAID, ChemIDplus,
|
||
NIST, NIST webbook, MOLI/NCI, ChemBank, MMDB, KEGG, and more.
|
||
Substance information includes chemical structures, synonyms,
|
||
vregistration IDs, description, related urls, database
|
||
cross-reference links, etc.</li></ul></td -->
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PubChemCompound"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=pccompound">PubChem
|
||
Compound</a> - A database made by NCBI and derived from PCSubstance.
|
||
It is a non-redundant view of the chemically validated substances in PubChem Substance.
|
||
There is one PubChem Compound record for each unique substance, and for each
|
||
unique substance component. There can be multiple PubChem Substance records
|
||
associated with one PubChem Compound record.
|
||
PubChem Compound contains all standardized structures, mixture components,
|
||
and precalculated structure neighboring links.
|
||
Compound information includes structure, compound property
|
||
information (molecular weight, formula, xLogP, count of the
|
||
rotatable bonds, H bond donor, H bond acceptor, etc.), and
|
||
structure description (SMILES, IUPAC name, INCHI).
|
||
</li></ul></td>
|
||
<!-- OLD DESCRIPTION, THROUGH 10/18/06:
|
||
td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=pccompound">PubChem
|
||
Compound</a> - A database made by NCBI and derived from PCSubstance.
|
||
It includes all the defined chemical components in PCSubstance.
|
||
It contains all standardized structures, mixture components,
|
||
and precalculated structure neighboring links.
|
||
Compound information includes structure, compound property
|
||
information (molecular weight, formula, xLogP, count of the
|
||
rotatable bonds, H bond donor, H bond acceptor, etc.), and
|
||
structure description (SMILES, IUPAC name, INCHI.).
|
||
</li></ul></td -->
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PubChemBioAssay"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=pcassay">PubChem
|
||
BioAssay</a> - The assay database consists of deposited bioactivity data
|
||
and descriptions of bioactivity assays used for screening of the chemical
|
||
substances contained in PubChem Substance, including descriptions of the
|
||
conditions and the readouts (bioactivity levels) specific to the screening procedure.
|
||
The assay database includes DTP/NCI's 710 million lines of in vitro
|
||
and in vivo data covering from cancer, HIV, to many other fields.
|
||
</li></ul></td>
|
||
<!-- OLD DESCRIPTION, THROUGH 10/18/06:
|
||
td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=pcassay">PubChem
|
||
BioAssay</a> - The assay database consists of deposited bioactivity data,
|
||
and assay description. The current assay database contains
|
||
DTP/NCI's 710 million lines of in vitro and in vivo data
|
||
covering from cancer, HIV, to many other fields.
|
||
</li></ul></td -->
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3">Structure-Related Tools - in addition to the structure databases
|
||
described above, NCBI offers several tools:
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Structure/CN3D/cn3d.shtml">Cn3D</a> - "See in
|
||
3-D," a structure and sequence alignment viewer for NCBI databases. It allows
|
||
viewing of 3-D structures and sequence-structure or structure-structure
|
||
alignments.
|
||
Cn3D can work as a helper application to your browser, or as a client-server
|
||
application that retrieves structure records from MMDB (described <a
|
||
href="#MMDB">above</a>) directly over the internet. The <a
|
||
href="/Structure/CN3D/cn3d.shtml">Cn3D home page</a> provides access to
|
||
information
|
||
on how to <a href="/Structure/CN3D/cn3dinstall.shtml">install</a> the program, a
|
||
<a
|
||
href="/Structure/CN3D/cn3dtut.shtml">tutorial</a> to get started, and a
|
||
comprehensive <a href="/Structure/CN3D/cn3dhelp.shtml">help
|
||
document</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Structure/cdd/wrpsb.cgi">CD-Search</a> -
|
||
The Conserved Domain Search Service (CD-Search) can be used to identify
|
||
the conserved domains present in a protein sequence. CD-Search
|
||
uses RPS-BLAST (described <a href="#RPS-BLAST">above</a>) to compare
|
||
a query sequence against position-specific score matrices that
|
||
have been prepared from conserved domain alignments present in
|
||
the Conserved Domain Database (CDD) (described <a href="#CDD">above</a>).
|
||
Hits can be displayed as a pairwise alignment of the query sequence
|
||
with a representative domain sequence, or as a multiple alignment.
|
||
Alignments are also mapped to known 3-dimensional structures,
|
||
and can be displayed using Cn3D (described <a href="#Cn3D">above</a>).
|
||
In the Cn3D display, residues in sequence alignments are variously colored,
|
||
based on their degree of conservation.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Structure/VAST/vast.html">VAST</a> - Vector
|
||
Alignment Search Tool - a computer algorithm developed at NCBI and used to
|
||
identify
|
||
similar protein 3-dimensional structures. The "structure neighbors" for every
|
||
structure in MMDB are pre-computed and accessible via links on the MMDB
|
||
Structure
|
||
Summary pages. These neighbors can be used to identify distant homologs that
|
||
cannot
|
||
be recognized by sequence comparison alone.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Structure/VAST/vastsearch.html">VAST
|
||
Search</a> -
|
||
structure-structure similarity search service. Compares 3D coordinates of a
|
||
newly
|
||
determined protein structure to those in the MMDB/PDB database. VAST Search
|
||
computes
|
||
a list of structure neighbors that you may browse interactively, viewing
|
||
superpositions and alignments by molecular graphics.</ul> </td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ================MOLECULAR DATABASES: GENES================ -->
|
||
<a NAME="Genes"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Genes</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<a NAME="EntrezGene"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> - Entrez
|
||
Gene provides a gene-based view of the data from a wide range of genomes. It
|
||
supplies key connections in the nexus of map, sequence, expression, structure,
|
||
functional, and homology data. Each record represents a single gene from a given
|
||
organism. The minimum set of data in a gene record includes a unique identifier
|
||
or GeneID assigned by NCBI, a preferred symbol, and any of sequence information,
|
||
map information, or official nomenclature from an authority list. In addition, a
|
||
gene record can also include expression, structure, functional, and homology data,
|
||
when available. Entrez Gene includes data from all organisms that have RefSeq
|
||
genome records (with NC_* accessions, see more info <a href="#RefSeq">above</a>),
|
||
and can also include data from recognized genome-specific databases that provide
|
||
NCBI with information about genes (preferably with defining sequence) or mapped
|
||
phenotypes. Entrez Gene is the successor to LocusLink (described <a
|
||
href="#LocusLink">below</a>).</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GeneRIF"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><blockquote><a
|
||
href="/projects/GeneRIF/GeneRIFhelp.html">GeneRIF</a> -
|
||
Gene References into Function (GeneRIFs) provide a simple mechanism to allow
|
||
scientists to add to the functional annotation of loci described in <a
|
||
href="/entrez/query.fcgi?db=gene">Entrez Gene</a>. They appear as annotated
|
||
bibliographies in Entrez Gene records, and consist of brief statements on gene
|
||
function with links to the corresponding PubMed records (<a
|
||
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Gr
|
||
aphi
|
||
cs&list_uids=4292">example: human MLH1</a>). The <a
|
||
href="/projects/GeneRIF/GeneRIFhelp.html">GeneRIF help page</a> describes the
|
||
simple steps
|
||
needed to submit information. GeneRIFs are also added to the Entrez Gene
|
||
records by
|
||
the MEDLINE Indexing Staff of the National Library of Medicine. GeneRIFs are
|
||
currently available for a subset of organisms in Entrez Gene, and will be
|
||
provided
|
||
for the loci of other organisms as the development of Entrez Gene
|
||
continues.</blockquote></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="LocusLink"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><blockquote><a href="/LocusLink/">LocusLink</a> - <b>LocusLink
|
||
was discontinued as of March 1, 2005.</b> It provided a foundation for what is
|
||
now Entrez Gene and was described in several articles (<a
|
||
href="/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11125071&dopt=Abstract">
|
||
Pruitt KD, Maglott DR (2001)</a>, <a
|
||
href="/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10637631&dopt=Abstract">
|
||
Pruitt KD, Katz KS, Sicotte H, Maglott DR (2000)</a>). It contained data for a
|
||
number of species such as human, mouse, rat, zebrafish, nematode, fruit fly, cow,
|
||
sea urchin, African clawed frog, HIV-1, and a few other model and commonly studied
|
||
organisms.
|
||
Data for these organisms (and from the ongoing collaboration among the groups
|
||
listed above) are now available in the <a
|
||
href="/entrez/query.fcgi?db=gene">Entrez Gene</a> database (described <a
|
||
href="#EntrezGene"">above</a>), which is the successor to LocusLink.
|
||
The <b>major differences between LocusLink and Entrez Gene</b> are scope of data
|
||
and
|
||
search interface. Entrez Gene contains data from all organisms with RefSeq genome
|
||
records. (RefSeq is <a href="#RefSeq">described </a> in the Molecular
|
||
Databases/Nucleotide Sequences section of this guide). Entrez Gene also uses the
|
||
Entrez search system, and therefore offers the helpful functions such as
|
||
Preview/Index, History, and LinkOut that are available for other Entrez databases.
|
||
The <a href="/entrez/query/static/help/genehelp.html">Entrez Gene help
|
||
document</a> includes numerous tips for previous users of LocusLink.
|
||
</blockquote>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CCDS"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/projects/CCDS/">Consensus CoDing Sequence (CCDS)
|
||
Database</a> - The CCDS project is a collaborative effort to identify a core set
|
||
of <b>human protein coding regions</b> that are consistently annotated and of high
|
||
quality. The long term goal is to support convergence towards a standard set of
|
||
gene annotations on the human genome. The collaborators include the
|
||
|
||
<a href="http://www.ncbi.nlm.nih.gov/">National Center for Biotechnology
|
||
Information</a> (NCBI, <a href="http://www.ncbi.nlm.nih.gov/mapview/">Map
|
||
Viewer</a>),
|
||
|
||
<a href="http://www.ebi.ac.uk/">European Bioinformatics Institute</a> (EBI, </a>
|
||
<a href="http://www.ensembl.org/">Ensembl</a>),
|
||
|
||
<a href="http://www.cbse.ucsc.edu/">University of California, Santa Cruz</a>
|
||
(UCSC, <a href="http://genome.ucsc.edu/cgi-bin/hgGateway">Genome Browser</a>), and
|
||
|
||
<a href="http://www.sanger.ac.uk/">Wellcome Trust Sanger Institute</a> (WTSI, <a
|
||
href="http://vega.sanger.ac.uk/">Vega</a>).
|
||
|
||
They identify the position of protein-coding regions of genes that are (1)
|
||
annotated consistently on the human genome by all of the participating centers and
|
||
(2) supported by transcript evidence, use of canonical splice sites, and other
|
||
quality assurance measures. Additional information about the curation, process
|
||
flow, and quality testing is available on the CCDS web site.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="UniGene"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/">UniGene</a> - ESTs and full-length mRNA
|
||
sequences organized into clusters that each represent a unique known or putative
|
||
gene within the organism from which the sequences were obtained. UniGene
|
||
clusters
|
||
are annotated with mapping and expression information when possible (e.g., for
|
||
human), and include cross-references to other resources. Sequence data can be
|
||
downloaded by cluster through the UniGene web pages, or the complete data set
|
||
can be
|
||
downloaded from the <a
|
||
href="ftp://ftp.ncbi.nih.gov/repository/UniGene/">repository/UniGene</a>
|
||
directory
|
||
of the FTP site. In addition, <b>UniGene DDD</b> (described <a
|
||
href="#UniGeneDDD">below</a>) can be used to show differential expression of
|
||
genes
|
||
between cDNA libraries. The <b>organisms represented</b> in UniGene are listed
|
||
on
|
||
the <a href="/UniGene/">UniGene home page</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="HomoloGene"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/HomoloGene/">HomoloGene</a> - a gene homology tool
|
||
that
|
||
compares nucleotide sequences between pairs of organisms in order to identify
|
||
putative orthologs. Curated orthologs are incorporated from a variety of
|
||
sources
|
||
via Entrez Gene. Organisms represented are listed on the HomoloGene home
|
||
page.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://mgc.nci.nih.gov/">Mammalian Gene Collection
|
||
(MGC)</a> - The NIH Mammalian Gene Collection (MGC) is a trans-NIH initiative
|
||
that
|
||
seeks to identify and sequence a representative full open reading frame (FL-ORF)
|
||
clone for each human, mouse, and rat gene. The MGC project entails the
|
||
production
|
||
of cDNA libraries and sequences, database and repository development, as well as
|
||
the
|
||
support of research for improved library construction, sequencing, and analytic
|
||
technologies. All the resources generated by the MGC are publicly accessible to
|
||
the
|
||
biomedical research community.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/RefSeq/HIVInteractions/">HIV Interactions</a> - The
|
||
HIV-1, Human Protein Interaction Database contains information about known
|
||
interactions of HIV-1 proteins with proteins from human hosts. It provides
|
||
annotated bibliograhies of published reports of protein interactions, with links
|
||
to
|
||
the corresponding PubMed records and sequence data. <a
|
||
href="#HIVInteractions">More
|
||
information</a> about this database is provided under "Literature Databases".
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="AceView"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/IEB/Research/Acembly/">AceView (Acembly)</a> - AceView
|
||
offers an integrated view of the human, nematode and Arabidopsis genes
|
||
reconstructed by co-alignment of all publicly available mRNAs and ESTs on the
|
||
genome sequence. The goals are to offer a reliable up-to-date resource on the
|
||
genes and their functions and to stimulate further validating experiments at the
|
||
bench. AceView carefully computes co-alignment and clustering of experimental
|
||
cDNA sequences, no prediction is involved. The resulting AceView genes and their
|
||
alternative variants are analyzed in terms of expression, intron-exon structure,
|
||
alternative features, regulation and neighbor relationships; the protein products
|
||
are analyzed for completeness, their best covering clones are identified, the
|
||
proteins are searched for motifs, membership to a protein family, conservation in
|
||
evolution, closest homologues in other species and signals for subcellular
|
||
localization. The genes are presented in the context of biological annotations
|
||
gathered from various sources. AceView can be queried by meaningful words or
|
||
sentences as well as by most standard identifiers.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<br>
|
||
|
||
<!-- ================MOLECULAR DATABASES: EXPRESSION================ -->
|
||
<a NAME="Expression"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Expression</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<a NAME="GEO"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/geo/">Gene Expression Omnibus (GEO)</a> - a gene
|
||
expression and hybridization array data repository, as well as a curated, online
|
||
resource for gene expression data browsing, query and retrieval. GEO was the
|
||
first
|
||
fully public high-throughput gene expression data repository, and became
|
||
operational
|
||
in July 2000. Many types of gene expression data from platforms such as spotted
|
||
microarray (microarray), high-density oligonucleotide array (HDA), hybridization
|
||
filter (filter) and serial analysis of gene expression (SAGE) data, are
|
||
accepted,
|
||
accessioned, and archived as a public data set. GEO data can be accessed
|
||
through
|
||
several search and browsing tools on the <a href="/geo/">GEO home page</a>, <a
|
||
href="/Entrez/">Entrez</a> (via <a href="/entrez/query.fcgi?db=geo">Entrez GEO
|
||
Profiles</a> and <a href="/entrez/query.fcgi?db=gds">Entrez GDS (GEO
|
||
DataSets)</a>),
|
||
and the <a href="ftp://ftp.ncbi.nih.gov/pub/geo/">FTP site</a>. The Tools/Gene
|
||
Expression section of this file provides information about <a
|
||
href="#GeneExpressionTools">data visualization and exploration capabilities</a>
|
||
available in GEO.<br></td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="GENSAT"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=gensat">GENSAT</a> - The Gene
|
||
Expression Nervous System Atlas, or GENSAT, project aims to map the expression
|
||
of
|
||
genes in the central nervous system of the mouse, using both in situ
|
||
hybridization
|
||
and transgenic mouse techniques. The GENSAT database contains a series of
|
||
images
|
||
related to gene expression experiments. The images are indexed on a number of
|
||
fields
|
||
relevant to biological discovery. Search criteria include gene names, gene
|
||
symbols,
|
||
gene aliases and synonyms, mouse ages, and imaging protocols. The GENSAT
|
||
project is
|
||
a collaboration among the <a href="http://www.ninds.nih.gov/">National Institute
|
||
of
|
||
Neurological Disorders and Stroke (NINDS)</a>, <a
|
||
href="http://www.gensat.org/index.html">Rockefeller University</a>, <a
|
||
href="http://www.stjudebgem.org/web/mainPage/mainPage.php">St. Jude Children's
|
||
Research Hospital</a>, and <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><FONT CLASS="Text">Expression-Related Tools</FONT> - in
|
||
addition to
|
||
the GEO database, described above, NCBI offers several tools:
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SAGEmap"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/SAGE/">SAGEmap</a> - Serial Analysis of Gene
|
||
Expression, or SAGE, is an experimental technique designed to quantitatively
|
||
measure
|
||
gene expression. SAGEmap is an online tool to compare computed gene expression
|
||
profiles between SAGE libraries generated by the Cancer Genome Anatomy Project
|
||
(<b>CGAP</b>, <a href="#CGAP">described</a> under <a
|
||
href="#CancerResearch">human
|
||
genome/cancer research</a>) and submitted by others through the Gene Expression
|
||
Omnibus (<b>GEO</b>, described <a href="#GEO">above</a>). SAGEmap also includes
|
||
a
|
||
comprehensive analysis of SAGE tags in human GenBank records, in which a UniGene
|
||
identifier is assigned to each human sequence that contains a SAGE tag. Data can
|
||
be
|
||
retrieved by tag, by sequence, by UniGene cluster ID and by library name. When
|
||
retrieving data by sequence or UniGene cluster ID, follow a SAGE tag's hotlink
|
||
to
|
||
find out its expression level in different SAGE libraries, and how it is
|
||
represented
|
||
in the rest of the sequences in GenBank. Retrieving data by library name takes
|
||
one
|
||
to GEO, where all SAGEmap data has been stored by library. Analytical tools
|
||
include
|
||
<a href="/SAGE/index.cgi?cmd=expsetup">xProfiler</a>, which compares gene
|
||
expression
|
||
between SAGE libraries of your choice as well as uploaded data. More
|
||
information
|
||
about the additional analytical capabilities of the SAGEmap resource is provided
|
||
in
|
||
the <a href="#GeneExpressionTools">tools/gene expression</a> section of this
|
||
file.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/ncicgap/">CGAP</a> - Cancer Genome Anatomy
|
||
Project - interdisciplinary program to identify the human genes expressed in
|
||
different cancerous states, based on cDNA (EST) libraries, and to determine the
|
||
molecular profiles of normal, precancerous, and malignant cells. Collaboration
|
||
among the National Cancer Institute, the NCBI, and numerous research labs.
|
||
Additional information about CGAP is provided in the <a
|
||
href="#GeneExpressionTools">tools/gene expression</a> section of this file.
|
||
Related
|
||
resources are described in the <a href="#CancerResearch">human genome/cancer
|
||
research</a> section.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/UniGene/info_ddd.shtml">UniGene DDD</a> -
|
||
Digital
|
||
Differential Display - an online tool to compare computed gene expression
|
||
profiles
|
||
between selected cDNA libraries. Using a statistical test, genes whose
|
||
expression
|
||
levels differ significantly from one tissue to the next are identified and shown
|
||
to
|
||
the user. <a href="#UniGene">Additional information</a> about UniGene is in the
|
||
<a
|
||
href="#Genes">molecular databases/genes</a> section.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<br>
|
||
|
||
<!-- ================MOLECULAR DATABASES: TAXONOMY================ -->
|
||
<a NAME="Taxonomy"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Taxonomy</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Taxonomy/">NCBI Taxonomy Database Home</a> - general
|
||
information about the Taxonomy project, including taxonomic resources and a list
|
||
of
|
||
outside curators collaborating with NCBI taxonomists. The NCBI Taxonomy
|
||
Database
|
||
contains the names and lineages of >160,000 organisms, both living and extinct,
|
||
that
|
||
are represented in the genetic databases with at least one nucleotide or protein
|
||
sequence. New organisms are added to the database as sequence data are
|
||
deposited
|
||
for them. The purpose of the taxonomy project at NCBI is to build a consistent
|
||
phylogenetic taxonomy for the sequence databases.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Taxonomy/">Taxonomy Browser</a> - The search bar on
|
||
the
|
||
Taxonomy home page allows you to browse the NCBI taxonomy database. Enter the
|
||
scientific or common name of a species (e.g., <i>Canis familiaris</i> or dog) or
|
||
a
|
||
higher taxon (e.g., Canidae) to view that organism or taxon's lineage; retrieve
|
||
the
|
||
available nucleotide, protein, structure, and genome records; and browse up and
|
||
down
|
||
the taxonomic tree. (<i>Tip</i>: For the broadest search results, select
|
||
the
|
||
"token set" option in the search bar, which searches for any string, whether in
|
||
the
|
||
beginning, middle, or end of a word.) <a
|
||
href="/entrez/query.fcgi?db=Taxonomy">Entrez</a> also provides an interface for
|
||
browsing the taxonomy database, and offers features such as the <a
|
||
href="/Taxonomy/CommonTree/wwwcmt.cgi">Common Tree</a> function, which allows
|
||
you to
|
||
build a tree for your own selection of organisms or taxa (<a
|
||
href="/Taxonomy/CommonTree/cmthelp.html">more...</a>).</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="TaxonomyBLASTb">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/blast/taxblasthelp.html">Taxonomy BLAST</a> - an
|
||
implementation of Gapped BLAST (2.x) that groups hits by source organism,
|
||
according
|
||
to information in NCBI's Taxonomy database. Species are listed in order of
|
||
sequence
|
||
similarity to the query sequence; the strongest match listed first. Three report
|
||
views are available:
|
||
<ul>
|
||
<li><i>organism report</i> - sorts the BLAST hits according to species, so that
|
||
all
|
||
of the hits to the same organism will appear together
|
||
<li><i>lineage report</i> - gives a simplified view of the relationships between
|
||
the
|
||
organisms, according to their classification in the taxonomy database. This
|
||
report
|
||
is "focused" on the organism which yielded the strongest BLAST hit. It answers
|
||
the
|
||
question, "how closely are the organisms in the BLAST hit list related to the
|
||
query
|
||
sequence according to the taxonomy database?"
|
||
<li><i>taxonomy report</i> - provides a more detailed report about the
|
||
relationships among all of the organisms found in the BLAST hit list, including
|
||
a
|
||
summary of the taxa that are represented, the number of species and subspecies,
|
||
and
|
||
the number of BLAST hits at each node in the taxonomic hierarchy.
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/taxik2.cgi">TaxPlot</a> - a tool for 3-way
|
||
comparisons of genomes on the basis of the protein sequences they encode. To use
|
||
TaxPlot, one selects a reference genome to which two other genomes are compared.
|
||
Pre-computed BLAST results are then used to plot a point for each predicted
|
||
protein
|
||
in the reference genome, based on the best alignment with proteins in each of
|
||
the
|
||
two genomes being compared.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ==========================END_DATABASES======================== -->
|
||
|
||
<!-- ===========================LITERATURE========================== -->
|
||
<a NAME="Literature"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" class="H3a">Literature Databases</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a
|
||
href="/Literature/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<a NAME="PubMed"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/">PubMed</a> - A database of citations and
|
||
abstracts for biomedical literature. These citations are from MEDLINE and
|
||
additional life science journals. PubMed also includes links to many sites
|
||
providing
|
||
full text articles and other related resources. PubMed is accessible through
|
||
the <a
|
||
href="/Entrez/">Entrez</a> search and retrieval system (<a
|
||
href="#Entrez">described
|
||
below</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Journals"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=journals">Journals
|
||
Database</a> - allows you to lookup journals that are cited in any of the Entrez
|
||
databases, including PubMed. Journals can be searched using the journal title,
|
||
MEDLINE or ISO abbreviation, ISSN, or the NLM Catalog ID.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MeSH"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=mesh">MeSH</a> - The
|
||
Medical
|
||
Subject Headings (MeSH) database is NLM's controlled vocabulary used for
|
||
indexing
|
||
articles for MEDLINE/PubMed. MeSH terminology provides a consistent way to
|
||
retrieve
|
||
information that may use different terminology for the same
|
||
concepts.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CitationMatcher"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT">
|
||
|
||
<ul><li><a href="/entrez/query/static/overview.html#Citation Matcher">Citation
|
||
Matcher</a> - allows you to find the PubMed ID of any article in the PubMed
|
||
database, given its bibliographic information (journal, volume, page,
|
||
etc.).</li>
|
||
|
||
<ul>
|
||
<li><a href="/entrez/query/static/citmatch.html">Citation Matcher for single
|
||
articles</a></i></li>
|
||
<li><a href="/entrez/getids.cgi">Batch Citation Matcher for many
|
||
articles</a></i></li>
|
||
<!-- li><FONT color="0033CC">E-Mail Citation Matcher</FONT> is also
|
||
available,
|
||
and can be used for or one or many articles. To obtain the help documentation,
|
||
send
|
||
the word HELP in the body of a message to the server address: <a
|
||
href="mailto:citation_matcher@ncbi.nlm.nih.gov">citation_matcher@ncbi.nlm.nih.go
|
||
v</a
|
||
></i></li -->
|
||
</ul>
|
||
|
||
</ul>
|
||
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="PubRef"></a>
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/entrez/query/static/help/pmhelp.html#Subsets">PubRef</a>
|
||
- a database of bibliographic records from a broad range of scientific journals,
|
||
and
|
||
links (when available) to full text on publisher web sites. PubRef includes
|
||
PubMed,
|
||
plus publisher supplied citations and abstracts from journals of other
|
||
scientific
|
||
disciplines. It is therefore is a superset of PubMed, and can be searched
|
||
through
|
||
the Entrez/PubMed system. The <a
|
||
href="/entrez/query/static/help/pmhelp.html#Subsets">PubMed Help document</a>
|
||
provides information on how to select PubRef for searching.</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<a NAME="PubMedCentral"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://www.pubmedcentral.nih.gov/">PubMed Central</a>
|
||
- a digital archive of biomedical and life sciences journal literature, including
|
||
clinical medicine and public health, managed by the National Center for
|
||
Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
|
||
It is not a journal publisher. Access to PubMed Central (PMC) is free and unrestricted.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="OMIM"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=OMIM">OMIM - Online <i>Mendelian
|
||
Inheritance in Man</i></a> - continuously updated catalog of human genes and
|
||
genetic
|
||
disorders, with links to associated literature references, sequence records,
|
||
maps,
|
||
and related databases.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Books"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=books">Entrez Books</a> - In
|
||
collaboration with book publishers, the NCBI is adapting textbooks for the web
|
||
and
|
||
linking them to PubMed, the biomedical bibliographic database. The idea is to
|
||
provide background information to PubMed, so that users can explore unfamiliar
|
||
concepts found in PubMed search results.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="HIVInteractions"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/RefSeq/HIVInteractions/">HIV Interactions</a> - The
|
||
HIV-1, Human Protein Interaction Database contains information about known
|
||
interactions of HIV-1 proteins with proteins from human hosts. <a
|
||
href="/RefSeq/">RefSeq</a> protein sequence records serve as anchors for
|
||
collecting
|
||
published information about interactions between HIV-1 and human proteins. Each
|
||
HIV
|
||
Interactions database record lists an HIV protein and the human proteins with
|
||
which
|
||
it has been found to interact. In turn, the Entrez Gene record
|
||
for
|
||
each human protein contains annotated HIV-1 Interactions bibliographies, which
|
||
consist of brief statements on protein interactions with links to the
|
||
corresponding
|
||
PubMed records and sequence data. The HIV Interactions database is a
|
||
collaborative
|
||
project among the developers of <a href="/RefSeq/">RefSeq</a> (<a
|
||
href="#RefSeq">description</a>) and <a href="/entrez/query.fcgi?db=gene">Entrez
|
||
Gene</a> (<a href="#EntrezGene">description</a>), and is similar in concept to
|
||
<a
|
||
href="/projects/GeneRIF/GeneRIFhelp.html">GeneRIF</a> (<a
|
||
href="#GeneRIF">description</a>).
|
||
In contrast to GeneRIFs for single genes, however, the publications cited in
|
||
the
|
||
HIV Interactions Database contain statements about binding between two proteins
|
||
rather than statements about the function of a single gene.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
<!-- ============================END_LITERATURE======================= -->
|
||
|
||
<!-- ======================GENOMES_AND_MAPS======================== -->
|
||
<a NAME="Genomes"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" CLASS="H3a">Genomes and Maps</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a" valign="top"><a
|
||
href="/Genomes/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="88%" BGCOLOR="#FFFFFF">
|
||
<blockquote>
|
||
<a href="#MultipleOrganisms">organism collections</a> (including
|
||
<a href="#EntrezGenome">Entrez Genome</a>,
|
||
<a href="#EntrezGenomeProject">Entrez Genome Project</a>,
|
||
<a href="#MapViewer">Map Viewer</a>,
|
||
<a href="#GenomesEntrezGene">Entrez Gene</a>,
|
||
<a href="#GenomesUniGene">UniGene</a>,
|
||
<a href="#GenomesHomoloGene">HomoloGene</a>, and
|
||
<a href="#COGs">COGs</a>), and organism-specific resources, such as:
|
||
<a href="#HumanGenome">human</a>,
|
||
<a href="#MouseGenome">mouse</a>,
|
||
<a href="#RatGenome">rat</a>,
|
||
<a href="#ZebrafishGenome">zebrafish</a>,
|
||
<a href="#DrosophilaGenome"><i>Drosophila</i></a>,
|
||
<a href="#NematodeGenome">nematode</a>,
|
||
<a href="#PlantGenomes">plant genomes</a>,
|
||
<a href="#YeastGenome">yeast</a>,
|
||
<a href="#MalariaGenome">malaria</a>,
|
||
<a href="#MicrobialGenomes">microbial genomes</a>,
|
||
<a href="#ViralGenomes">viruses</a>,
|
||
<a href="#ViroidGenomes">viroids</a>,
|
||
<a href="#Plasmids">plasmids</a>,
|
||
<a href="#EukaryoticOrganelles">eukaryotic organelles</a>
|
||
</blockquote>
|
||
</td>
|
||
<td CLASS="TEXT" WIDTH="12%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- =========CATEGORY WITHIN GENOMES_AND_MAPS: MULTIPLE ORGANISMS======= -->
|
||
<a NAME="MultipleOrganisms"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Organism Collections</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<a NAME="GenomicBiology"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Genomes/">Genomic Biology</a> -
|
||
An introduction to the field of genomic biology, with links to the genome
|
||
resources pages for major organisms and organism groups, as well as links to
|
||
additional NCBI genome resources.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="EntrezGenome"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=Genome">Entrez Genome</a> -
|
||
sequence and map data from the whole
|
||
genomes of over 1000 organisms. The genomes represent both completely sequenced
|
||
organisms and those for which sequencing is in progress. All three main domains
|
||
of
|
||
life - <a
|
||
HREF="/genomes/static/eub_g.html">bacteria</a>,
|
||
<a
|
||
HREF="/genomes/static/a_g.html">archaea,</a>
|
||
and <a
|
||
HREF="/genomes/static/euk_g.html">eukaryota</a>
|
||
- are represented, as well as many <a
|
||
HREF="/genomes/VIRUSES/viruses.html">viruses</a>,
|
||
<a
|
||
HREF="/genomes/static/phg.html">phages</a>,
|
||
<a
|
||
HREF="/genomes/static/vid.html">viroids</a>,
|
||
<a
|
||
HREF="/genomes/static/o.html">plasmids</a>,
|
||
and <a
|
||
HREF="/genomes/ORGANELLES/organelles.html">organelles.</a>. Entrez Genome
|
||
provides
|
||
graphical overviews of complete genomes/chromosomes, and the ability to explore
|
||
regions of interest in progressively greater detail. <a
|
||
href="#ProtTaxTable">ProtTables and TaxTables</a> are provided for organisms on
|
||
which analyses have been done by NCBI staff. In addition, the <a
|
||
href="/mapview/">Map Viewer</a>, a software component of Entrez Genome, provides
|
||
views of integrated chromosome maps for a variety of organisms (see additional
|
||
information about the Map Viewer <a href="#MapViewer">below</a>).
|
||
<blockquote>Information about submitting genome data from complete genomes is
|
||
provided in the Resource Guide section on <a href="#SubmitGenomes">Submission of
|
||
complete genomes</a>. After data from complete genomes are submitted, they are
|
||
made available in Entrez Genome (as complete genomes or chromosomes) and Entrez
|
||
Nucleotide (as chromosome or genome fragments such as contigs). Entrez
|
||
Nucleotide also provides access to the records for complete genomes/chromosomes,
|
||
but the default view of those records is the Nucleotide database is GenBank
|
||
format, whereas the default view in Entrez Genome is a graphical overview. A
|
||
companion database, Entrez Genome Project, is <a
|
||
href="#EntrezGenomeProject">described</a> below.</blockquote></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="EntrezGenomeProject"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?DB=genomeprj">Entrez Genome
|
||
Project</a> -
|
||
a companion database to Entrez Genome (<a href="#EntrezGenome">described</a>
|
||
above). The actual data from genome sequencing projects are contained in Entrez
|
||
Genome (as complete genomes chromosomes) and Entrez Nucleotide (as chromosome or
|
||
genome fragments such as contigs). The Genome Project database, on the other
|
||
hand, provides an umbrella view of the status of each genome project, links to
|
||
project data in the other Entrez databases, and links to a variety of other NCBI
|
||
and external resources associated with a given genome project. A genome
|
||
project's status can be complete or in-progress, and the project can include
|
||
large-scale sequencing, assembly, annotation, and mapping efforts. New genome
|
||
sequencing projects can be registered through the <a
|
||
href="/genomes/mpfsubmission.cgi">Genome project submission form</a>. More
|
||
information about the submission of data from complete genomes is provided in
|
||
the Resource Guide section on <a href="#SubmitGenomes">Submission of complete
|
||
genomes</a>. (Although the Entrez Genome Project database does not include
|
||
viral genome sequencing projects, data from those projects are submitted to
|
||
GenBank and are available in the Entrez Nucleotide and Entrez Genome databases.
|
||
There is also a special set of resources at NCBI dedicated to <a
|
||
href="#ViralGenomes">Viral Genomes</a>.)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mailman/listinfo/genomes-announce">Genomes
|
||
Announcements</a> - To receive announcements about recently completed genomes,
|
||
see
|
||
the <a href="Summary/email_lists.html">NCBI Announcements Email Lists</a>
|
||
page.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MapViewer"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/">Map Viewer</a> - The Map Viewer is a
|
||
software
|
||
component of Entrez Genome (described <a href="#EntrezGenome">above</a>) that
|
||
provides special browsing capabilities for a subset of organisms. It allows you
|
||
to
|
||
view and search an organism's complete genome, display chromosome maps, and zoom
|
||
into progressively greater levels of detail, down to the sequence data for a
|
||
region
|
||
of interest. If multiple maps are available for a chromosome, it displays them
|
||
aligned to each other based on shared marker and gene names, and, for the
|
||
sequence
|
||
maps, based on a common sequence coordinate system. The organisms currently
|
||
represented in the Map Viewer are listed on the Map Viewer home page and in the
|
||
<a
|
||
href="/mapview/static/MapViewerHelp.html">Map Viewer help document</a>, which
|
||
provides general information on how to use that tool. The number and types of
|
||
available maps vary by organism, and are described in the "data and search tips"
|
||
file provided for each organism.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GenomesEntrezGene"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> - Entrez
|
||
Gene
|
||
provides a gene-based view of the data from a wide range of genomes. It
|
||
supplies
|
||
key connections in the nexus of map, sequence, expression, structure,
|
||
functional,
|
||
and homology data. Each record represents a single gene from a given organism.
|
||
The
|
||
minimum set of data in a gene record includes a unique identifier or GeneID
|
||
assigned
|
||
by NCBI, a preferred symbol, and any of sequence information, map information,
|
||
or
|
||
official nomenclature from an authority list. In addition, a gene record can
|
||
also
|
||
include expression, structure, functional, and homology data, when available.
|
||
Entrez Gene includes data from all organisms that have RefSeq genome records
|
||
(with
|
||
NC_* accessions, see more info <a href="#RefSeq">above</a>), and can also
|
||
include
|
||
data from recognized genome-specific databases that provide NCBI with
|
||
information
|
||
about genes (preferably with defining sequence) or mapped phenotypes.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GenomesUniGene"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/">UniGene</a> - ESTs and full-length mRNA
|
||
sequences organized into clusters that each represent a unique known or putative
|
||
gene within the organism from which the sequences were obtained. UniGene
|
||
clusters
|
||
are annotated with mapping and expression information when possible (e.g., for
|
||
human), and include cross-references to other resources. Sequence data can be
|
||
downloaded by cluster through the UniGene web pages, or the complete data set
|
||
can be
|
||
downloaded from the <a
|
||
href="ftp://ftp.ncbi.nih.gov/repository/UniGene/">repository/UniGene</a>
|
||
directory
|
||
of the FTP site. In addition, UniGene DDD (described <a
|
||
href="#UniGeneDDD">below</a>) can be used to show differential expression of
|
||
genes
|
||
between cDNA libraries. The organisms represented in UniGene are listed on the
|
||
<a
|
||
href="/UniGene/">UniGene home page</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="GenomesHomoloGene"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/HomoloGene/">HomoloGene</a> - a gene homology tool
|
||
that
|
||
compares nucleotide sequences between pairs of organisms in order to identify
|
||
putative orthologs. Curated orthologs are incorporated from a variety of
|
||
sources
|
||
via Entrez Gene. Organisms represented are listed on the HomoloGene home
|
||
page.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="COGs"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/COG/">COGs - Clusters of Orthologous Groups</a> -
|
||
natural
|
||
system of gene families from complete genomes. Clusters of Orthologous Groups
|
||
(COGs) were delineated by comparing protein sequences encoded in complete
|
||
unicellular genomes representing 30 major phylogenetic lineages. Each COG
|
||
consists
|
||
of individual proteins or groups of paralogs from at least 3 lineages and thus
|
||
corresponds to an ancient conserved domain. The <a href="/COG/old/">Initial
|
||
Version</a> of COGs includes 44 organisms. The <a href="/COG/new/">Updated
|
||
Version</a> of COGs includes 66 organisms in the <a
|
||
href="/COG/new/release/phylox.cgi">Unicellular Clusters</a>, plus <a
|
||
href="/COG/new/shokog.cgi">Eukaryotic Clusters</a> (called KOGs). More
|
||
organisms
|
||
will be added in the future.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Entrez/Genome/org.html">Download Genomes <350 KB</a>
|
||
via
|
||
Entrez Genome pages for individual organisms</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/">Download
|
||
Genomes
|
||
>350 KB from the NCBI ftp site</a> - see FTP information <a
|
||
href="#FTP_HumanGenome">below</a>; ftp links are also available from Entrez
|
||
Genome
|
||
pages for individual organisms</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/static/links.html">Genome Sequencing
|
||
Centers</a>
|
||
- list of genome sequencing centers and the organisms on which they work</td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS TABLE: HUMAN======== -->
|
||
<a NAME="HumanGenome"></a>
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Human Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="95%" BGCOLOR="#FFFFFF">
|
||
<blockquote>
|
||
<a href="#HumanGenomeGuide">Guide</a>,
|
||
<a href="#HumanChromosomes">Chromosomes</a>,
|
||
<a href="#HumanSequences">Sequences</a>,
|
||
<a href="#HumanGenes">Genes</a>,
|
||
<a href="#HumanGenomeBLAST">BLAST</a>,
|
||
<a href="#Clones">Clones</a>,
|
||
<a href="#HumanMaps">Genome Maps</a>,
|
||
<a href="#HumanMappedMarkers">Mapped Markers</a>,
|
||
<a href="#HumanCytogenetics">Cytogenetics</a>,
|
||
<a href="#HumanGeneExpression">Gene Expression</a>,
|
||
<a href="#HumanGeneticVariation">Genetic Variation</a>,
|
||
<a href="#HumanDisorders">Disorders</a>,
|
||
<a href="#CancerResearch">Cancer Research</a>,
|
||
<a href="#HumanGenomeFTP">FTP</a>
|
||
</blockquote>
|
||
</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: GUIDE======== -->
|
||
|
||
<a NAME="HumanGenomeGuide"></a>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Guide</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/guide/">Human Genome Resources
|
||
Guide</a> -
|
||
overview of available human genome data resources. Includes bulletins and
|
||
progress
|
||
reports concerning the Human Genome Project and
|
||
provides centralized access to previously disparate data.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/About/Doc/hs_genomeintro.html">Introduction
|
||
to
|
||
NCBI's Genome Resource</a> - overview of the nature of data generated by the
|
||
human
|
||
genome project, the processes use to assemble and annotate the data, and to
|
||
integrate it with a wide range of information from other
|
||
resources.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="HumanContigAssembly"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/guide/build.html">NCBI Contig Assembly
|
||
and
|
||
Annotation Process</a> - describes the processes use to assemble contigs from
|
||
the
|
||
high throughput genomic sequences (HTGs, described <a href="#HTG">above</a>),
|
||
and to
|
||
annotate the contigs with features. It also describes the various resources
|
||
that
|
||
can be used to access the human genome data.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Tour/">Tour of the Draft Human Genome
|
||
Sequence</a> - provides an introduction to how the
|
||
draft sequence of the human genome can be used by biologists, and includes
|
||
examples
|
||
of the types of questions that can be answered with the data.</li></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: CHROMOSOMES======== -->
|
||
|
||
<a NAME="HumanChromosomes"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Chromosomes</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="HumanChromosomeMapViews"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/mapview/map_search.cgi?taxid=9606">Map
|
||
Viewer</a>
|
||
- <b>integrated views of chromosome maps</b> - The Map Viewer (described <a
|
||
href="#MapViewer">above</a>) displays one or more maps which have been aligned
|
||
to
|
||
each other based on shared marker and gene names, and, for the sequence maps,
|
||
based
|
||
on a common sequence coordinate system. For human, the Map Viewer includes >20
|
||
sequence, cytogenetic, genetic linkage, radiation hybrid, and other maps.
|
||
(When viewing a chromosome, use the "Maps & Options" dialog box to display
|
||
the
|
||
map(s) of interest.) The sequence maps are based on the contigs
|
||
built
|
||
from the draft and finished sequence data generated by the Human Genome Project.
|
||
A
|
||
<a href="/mapview/static/humansearch.html">list of available human maps</a> and
|
||
their descriptions is provided. The <a
|
||
href="/mapview/static/MapViewerHelp.html">Map Viewer help document</a> provides
|
||
general information on how to use that tool. Information about the <a
|
||
href="/genome/guide/build.html">NCBI Contig Assembly and Annotation Process</a>
|
||
is
|
||
also available.<p></p></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="#HumanGenomeFTP">FTP human chromosome data</a>
|
||
-
|
||
see the FTP information, <a href="#HumanGenomeFTP">below</a></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: SEQUENCES======== -->
|
||
|
||
<a NAME="HumanSequences"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Sequences</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="HumanGenomeSequencing"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/seq/">Human Genome Sequencing</a> -
|
||
sequencing progress of the Human Genome Project; links to chromosome views in
|
||
the
|
||
<b>Map Viewer</b> (described <a href="#HumanChromosomeMapViews">above</a>),
|
||
including <a href="/mapview/static/humansearch.html#SequenceMaps">sequence
|
||
maps</a>
|
||
assembled from contigs that were constructed (<a
|
||
href="/genome/guide/build.html">more...</a>) from international sequencing
|
||
center
|
||
data; list of <a href="/genome/seq/HsCenters.html">genome sequencing
|
||
centers</a>.</font></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/RefSeq/">RefSeq</a> - NCBI database of
|
||
Reference
|
||
Sequences. Curated, non-redundant set including genomic DNA contigs, mRNAs and
|
||
proteins for known genes, mRNAs and proteins for gene models, and entire
|
||
chromosomes. Accession numbers have the format of two letters, an underscore
|
||
bar,
|
||
and six digits, for example, NC_123456, NT_123456, NM_123456, NP_123456 (more
|
||
info
|
||
about <a href="/RefSeq/key.html#accession">accession numbers</a> and <a
|
||
href="/RefSeq/RSfaq.html#access">access</a>).</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="EntrezHuman"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Entrez/">Entrez</a> - provides integrated
|
||
access
|
||
to nucleotide and protein sequence data in GenBank, EMBL, DDBJ, RefSeq,
|
||
PIR-International, PRF, Swiss-Prot, and PDB, along with
|
||
3D protein structures, genomic mapping information, and PubMed MEDLINE. Entrez
|
||
contains pre-computed similarity searches for each database record, producing a
|
||
list of related sequences, structures, and MEDLINE records. Includes sequence
|
||
data
|
||
from >160,000 species; use the organism field to limit searches to human
|
||
records.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/UniGene/Hs.Home.html">UniGene</a> - ESTs and
|
||
full-length mRNA sequences organized into clusters that each represent a unique
|
||
known or putative gene within the organism from which the sequences were
|
||
obtained.
|
||
Additional information about UniGene is provided <a
|
||
href="#UniGene">above</a><!--
|
||
(in both the "<a href="#Nucleotides">Nucleotide Sequences</a>" and "<a
|
||
href="#Genomes">Genomes and Maps</a>/<a href="#MultipleOrganisms">Organism
|
||
Collections</a>" sections) -->.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/dbEST/index.html">dbEST</a> - Database of
|
||
Expressed Sequence Tags - short (about 300-500 bp) cDNA sequences representing
|
||
single-pass reads from mRNA. Usually produced in large numbers and represent a
|
||
snapshot of the genes expressed in a given tissue, and/or at a given
|
||
developmental
|
||
stage. Also includes ESTs generated by the <a href="#CGAP">CGAP</a> project
|
||
(see <a
|
||
href="#CancerResearch">Cancer Research</a>, below), and sequences from
|
||
differential
|
||
display and RACE experiments.</li></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: GENES======== -->
|
||
|
||
<a NAME="HumanGenes"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Genes</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/projects/CCDS/">Consensus CoDing Sequence
|
||
(CCDS)
|
||
Database</a> - The CCDS project is a collaborative effort to identify a core set
|
||
of <b>human protein coding regions</b> that are consistently annotated and of high
|
||
quality. The long term goal is to support convergence towards a standard set of
|
||
gene annotations on the human genome. The collaborators include the
|
||
|
||
<a href="http://www.ncbi.nlm.nih.gov/">National Center for Biotechnology
|
||
Information</a> (NCBI, <a href="http://www.ncbi.nlm.nih.gov/mapview/">Map
|
||
Viewer</a>),
|
||
|
||
<a href="http://www.ebi.ac.uk/">European Bioinformatics Institute</a> (EBI, </a>
|
||
<a href="http://www.ensembl.org/">Ensembl</a>),
|
||
|
||
<a href="http://www.cbse.ucsc.edu/">University of California, Santa Cruz</a>
|
||
(UCSC, <a href="http://genome.ucsc.edu/cgi-bin/hgGateway">Genome Browser</a>), and
|
||
|
||
<a href="http://www.sanger.ac.uk/">Wellcome Trust Sanger Institute</a> (WTSI, <a
|
||
href="http://vega.sanger.ac.uk/">Vega</a>).
|
||
|
||
They identify the position of protein-coding regions of genes that are (1)
|
||
annotated consistently on the human genome by all of the participating centers and
|
||
(2) supported by transcript evidence, use of canonical splice sites, and other
|
||
quality assurance measures. Additional information about the curation, process
|
||
flow, and quality testing is available on the CCDS web site.</li></ul></td>
|
||
</tr>
|
||
|
||
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> -
|
||
a gene-based view of the data from a wide range of genomes, including human. It
|
||
supplies key connections in the nexus of map, sequence, expression, structure,
|
||
functional, and homology data. <a href="#EntrezGene">More information about
|
||
Entrez Gene</a> is provided above, in the Molecular Databases/Genes section.
|
||
</li></ul></td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=OMIM">OMIM</a> - Online
|
||
Mendelian Inheritance in Man - continuously updated catalog of human genes and
|
||
genetic disorders, with links to associated literature references, sequence
|
||
records,
|
||
maps, and related databases.</li></ul></td>
|
||
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/RefSeq/">RefSeq</a> - NCBI database of
|
||
Reference
|
||
Sequences. Curated, non-redundant set including genomic DNA contigs, mRNAs and
|
||
proteins for known genes, mRNAs and proteins for gene models, and entire
|
||
chromosomes. Accession numbers have the format of two letters, an underscore
|
||
bar,
|
||
and six digits, for example, NC_123456, NT_123456, NM_123456, NP_123456 (more
|
||
info
|
||
about <a href="/RefSeq/key.html#accession">accession numbers</a> and <a
|
||
href="/RefSeq/RSfaq.html#access">access</a>).</li></ul></td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/UniGene/Hs.Home.html">UniGene</a> - ESTs and
|
||
full-length mRNA sequences organized into clusters that each represent a unique
|
||
known or putative gene within the organism from which the sequences were
|
||
obtained.
|
||
Additional information about UniGene is provided <a
|
||
href="#UniGene">above</a><!--
|
||
(in both the "<a href="#Nucleotides">Nucleotide Sequences</a>" and "<a
|
||
href="#Genomes">Genomes and Maps</a>/<a href="#MultipleOrganisms">Organism
|
||
Collections</a>" sections) -->.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/HomoloGene/">HomoloGene</a> - a gene homology
|
||
tool that compares nucleotide sequences between pairs of organisms, including
|
||
human,
|
||
mouse, rat, zebrafish, and fruit fly, in order to identify putative orthologs.
|
||
Curated orthologs are incorporated from a variety of sources via
|
||
Entrez Gene.</li></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: BLAST======== -->
|
||
|
||
<a NAME="HumanGenomeBLAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">BLAST against human genomic sequence data</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/seq/HsBlast.html">BLAST against the
|
||
draft
|
||
human genome sequence</a> - Compare your nucleotide or protein query sequence to
|
||
the
|
||
working draft sequence of the human genome, its mRNA and protein products, or
|
||
the
|
||
other data sets described below. The genome sequence been assembled from
|
||
GenBank
|
||
sequence records (primarily HTGs) using the process described in <a
|
||
href="/genome/guide/build.html">NCBI Contig Assembly and Annotation Process</a>.
|
||
The contigs assembled by this process have been given NT_* accession numbers as
|
||
part
|
||
of the RefSeq project (described <a href="#RefSeq">above</a>).
|
||
|
||
<p>A <a href="/genome/seq/Database.html">variety of database choices</a> are
|
||
provided on the <a href="/genome/seq/HsBlast.html">Human Genome BLAST
|
||
page</a>.</p>
|
||
|
||
</ul></td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/BLAST/">BLAST against human ESTs</a> -
|
||
compare a
|
||
nucleotide or protein sequence against the human ESTs by choosing
|
||
<b>est_human</b>
|
||
as the database to be searched when using Nucleotide BLAST or Translated
|
||
BLAST.</li></ul></td>
|
||
</tr -->
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&HITLIST_SIZE=100&NCB
|
||
I_GI
|
||
=on&PAGE=Nucleotides&PROGRAM=blastn&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS
|
||
.y=8
|
||
&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes">BLAST against gss database</a> - compare a
|
||
nucleotide sequence against random "single pass read" <b>genome survey
|
||
sequences</b>
|
||
such as cosmid/BAC/YAC end sequences,
|
||
exon trapped genomic sequences, and Alu PCR sequences. Although the gss
|
||
database
|
||
contains sequences from many organisms, you can limit search results to
|
||
human.</li></ul></td>
|
||
</tr -->
|
||
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: CLONES======== -->
|
||
|
||
<a NAME="Clones"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Clones</FONT><img SRC="spacer10.GIF" width="440"
|
||
height="1" border="0"></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT2">
|
||
<blockquote><i>NCBI does not distribute clones. However, some NCBI resources
|
||
contain information about clones and the sources from which they can be
|
||
obtained.</i></blockquote>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CloneMaps"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li>Clone Maps -
|
||
various clone maps for human have been included in the <b>Map Viewer</b>,
|
||
described
|
||
<a href="#MapViewerHuman">below</a>. The document that describes the various <a
|
||
href="/mapview/static/humansearch.html">maps available for human</a> includes a
|
||
section listing the <a href="/mapview/static/humansearch.html#ObjectTypes">maps
|
||
that
|
||
contain clone information</a>. To select those maps for display, use the
|
||
Maps&Options dialog box when viewing any human chromosome. (Several other <a
|
||
href="/mapview/static/MapViewerHelp.html#OrganismList">organisms accessible</a>
|
||
through the <a href="/mapview/static/MVstart.html">Map Viewer</a> are
|
||
represented by
|
||
maps that contain clone information. The organism-specific "data and search
|
||
tips"
|
||
files provide additional detail about the maps available for each organism.)<!--
|
||
A
|
||
<a href="/mapview/static/humansearch.html">list of available maps</a> is
|
||
provided in
|
||
the associated help document, including those that show the positions of <a
|
||
href="/mapview/static/humansearch.html#ObjectTypeClone">clones</a>. When
|
||
viewing a
|
||
chromosome, use the "Maps & Options" dialog box to select the map(s) of
|
||
interest.
|
||
-->
|
||
</ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CloneRegistry"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/clone/">Clone Registry</a> - a
|
||
database
|
||
used by participating <a href="/genome/seq/HsCenters.html">human genome
|
||
sequencing
|
||
centers</a> and <a href="/genome/seq/MmSeqCenters.html">mouse genome sequencing
|
||
centers</a> to record which clones have been selected for sequencing, which are
|
||
currently in the pipeline, and which are finished and represented by sequence
|
||
entries in GenBank. Includes BACs, PACs, cosmids, fosmids. Uses <a
|
||
href="/genome/clone/nomenclature.shtml">standardized clone names</a> that
|
||
represents
|
||
a clone's microtitre plate address (plate number, row, and column) prefixed by a
|
||
library abbreviation, to produce unique names. Includes <a
|
||
href="/genome/clone/ordering.html">clone ordering
|
||
information</a>.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/cyto/hbrc.shtml">Human BAC
|
||
Resource</a> -
|
||
A cytogenetic resource of large-insert,
|
||
FISH-mapped clones containing sequence-tagged sites. Will help
|
||
integrate cytogenetic, radiation-hybrid, linkage, and sequence maps of
|
||
the human genome. Includes links to clone distributors.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MGC"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="http://mgc.nci.nih.gov/">Mammalian Gene
|
||
Collection
|
||
(MGC)</a> - The NIH Mammalian Gene Collection (MGC) is a trans-NIH initiative
|
||
that
|
||
seeks to identify and sequence a representative full open reading frame (FL-ORF)
|
||
clone for each human, mouse, and rat gene. The MGC project entails the
|
||
production
|
||
of cDNA libraries and sequences, database and repository development, as well as
|
||
the
|
||
support of research for improved library construction, sequencing, and analytic
|
||
technologies. All the resources generated by the MGC are publicly accessible to
|
||
the
|
||
biomedical research community.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ClonesNonHuman"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><blockquote><i><b>Clone Information for Other (Non-human)
|
||
Organisms</b> - Some organisms have additional clone information resources. For
|
||
example, the resources available for the <a href="#MouseGenome"><b>mouse
|
||
genome</b></a> include several items mentioned above, plus a <b>CloneFinder</b>,
|
||
described <a href="#MouseGenomeCloneFinder">below</a>. In addition, many
|
||
records in
|
||
dbEST (described <a href="#dbEST">above</a>) include information about clone
|
||
sources
|
||
such as the <a href="http://image.llnl.gov/">I.M.A.G.E.
|
||
consortium</a>.</i></blockquote></td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: MAPS======== -->
|
||
|
||
<a NAME="HumanMaps"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Genome Maps</FONT><img SRC="spacer10.GIF" width="440"
|
||
height="1" border="0"></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="/entrez/query.fcgi?cmd=Search&db=Genome&term=human[orgn]&dispmax=50&doptcmdl
|
||
=Summary">Entrez Genome</a> - links to the human chromosome views in
|
||
the
|
||
Map Viewer (details <a href="#MapViewerHuman">below</a>). Entrez Genome also
|
||
includes a view of the human mitochondrion (accessible under eukaryotic
|
||
organelles),
|
||
which can be viewed in its entirety or explored in progressively greater detail
|
||
(additional information about Entrez Genome <a
|
||
href="#EntrezGenome">above</a>).</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MapViewerHuman"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/mapview/map_search.cgi?taxid=9606">Map
|
||
Viewer</a>
|
||
- <b>integrated views of chromosome maps</b> - The Map Viewer is a software
|
||
component of Entrez Genome that displays one or more maps which have been
|
||
aligned
|
||
to each other based on shared marker and gene names, and, for the sequence maps,
|
||
based on a common sequence coordinate system. For human, the Map Viewer includes
|
||
>20
|
||
sequence, cytogenetic, genetic linkage, radiation hybrid, and other maps.
|
||
(When viewing a chromosome, use the "Maps & Options" dialog box to display
|
||
the
|
||
map(s) of interest.) The sequence maps are based on the contigs
|
||
built
|
||
from the draft and finished sequence data generated by the Human Genome Project.
|
||
A
|
||
<a href="/mapview/static/humansearch.html">list of available human maps</a> and
|
||
their descriptions is provided. The <a
|
||
href="/mapview/static/MapViewerHelp.html">Map Viewer help document</a> provides
|
||
general information on how to use that tool. Information about the <a
|
||
href="/genome/guide/build.html">NCBI Contig Assembly and Annotation Process</a>
|
||
is
|
||
also available.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GeneMap"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genemap/">GeneMap'99</a> - physical map of
|
||
>35,000 human gene-based markers, constructed by the International Radiation
|
||
Hybrid
|
||
Mapping Consortium using a consistent set of RH reagents and methodologies.
|
||
Provides a framework for accelerated sequencing efforts by highlighting key
|
||
landmarks (gene-rich regions) of the chromosomes, and represents the cooperative
|
||
efforts of more than one hundred scientists throughout the world.<br>
|
||
<font size="-1"><i>Note:</i> The GeneMap'99 data have also been included in the
|
||
<a
|
||
href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>, described <a
|
||
href="#EntrezMapViewer">above</a>. When viewing a chromosome, use the "Maps &
|
||
Options" dialog box to select the map(s) of interest.</font></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="NCBI_RH_map"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/rhmap/">NCBI RH Map</a> - NCBI
|
||
Integrated
|
||
Radiation Hybrid Map</a> contains 23,723 markers from both the G3 and GB4
|
||
RH panels of GeneMap'99. Those markers were mapped with respect to 1084
|
||
framework markers (a subset of markers common to the G3 and GB4 panels).
|
||
All markers from both panels were interpolated onto the GB4 scale.
|
||
The article by <a
|
||
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_
|
||
uids
|
||
=10720576&dopt=Abstract">R. Agarwala et al.</a> provides detail about
|
||
the integration strategy, as well as the methods used to evaluate the
|
||
quality of the integrated map.<br>
|
||
<font size="-1"><i>Note:</i> The NCBI RH Map data have also been included in the
|
||
<a
|
||
href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>, described <a
|
||
href="#EntrezMapViewer">above</a>. When viewing a chromosome, use the "Maps &
|
||
Options" dialog box to select the map(s) of interest.</font></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/Mitelman">Mitelman Database of
|
||
Chromosome
|
||
Aberrations in Cancer</a> - genome-wide map of chromosomal breakpoints in human
|
||
cancer, by Drs. Mitelman, Mertens, and Johansson (eds),
|
||
http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with
|
||
the
|
||
<a href="/CGAP/">Cancer Genome Anatomy Project (CGAP)</a>. <!-- Original
|
||
version of
|
||
the aberration summary was published in a special issue of Nature Genetics, Vol.
|
||
15(Spec. No.):417-74 (April 1997). --><br>
|
||
<font size="-1"><i>Note:</i> The Mitelman data have also been included in the <a
|
||
href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>, described <a
|
||
href="#EntrezMapViewer">above</a>. When viewing a chromosome, use the "Maps &
|
||
Options" dialog box to select the map(s) of interest.</font></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Omim/getmap.cgi?">OMIM Gene Map</a> -
|
||
cytogenetic locations of genes that have been reported in the literature and
|
||
determined by a variety of mapping methods. Can be searched by gene symbol or
|
||
cytogenetic chromosomal location. Accessible from the OMIM page (described <a
|
||
href="#OMIM">above</a>).<br>
|
||
<font size="-1"><i>Note:</i> The OMIM Gene Map data have also been included in
|
||
the
|
||
<a href="/mapview/static/humansearch.html#Genes_Cytogenetic">Genes_Cytogenetic
|
||
Map</a> of the <a href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>
|
||
(described <a href="#EntrezMapViewer">above</a>). When viewing a chromosome,
|
||
use
|
||
the "Maps & Options" dialog box to select the map(s) of
|
||
interest.</font></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Omim/getmorbid.cgi">OMIM Morbid
|
||
Map</a> -
|
||
alphabetical listing of diseases and corresponding cytogenetic map locations,
|
||
with
|
||
links to OMIM entries. Accessible from the OMIM page (described <a
|
||
href="#OMIM">above</a>).<br>
|
||
<font size="-1"><i>Note:</i> The OMIM Morbid Map data have also been included in
|
||
the
|
||
<a href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>, described <a
|
||
href="#EntrezMapViewer">above</a>. When viewing a chromosome, use the "Maps &
|
||
Options" dialog box to select the map(s) of interest.</font></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="HumanMouseMap"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Homology/">Human-Mouse Homology Maps</a> - a
|
||
table comparing genes in homologous segments of DNA from human and mouse, sorted
|
||
by
|
||
position in each genome. Computed by integrating orthologs identified at The
|
||
Jackson Laboratory with putative orthologs identified by sequence homology.
|
||
The <a href="/Homology/Davis/">original maps</a> by M. F. Seldin
|
||
of the University of California at Davis are also available.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: MAPPED MARKERS======== -->
|
||
|
||
<a NAME="HumanMappedMarkers"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Mapped Markers</FONT><img SRC="spacer10.GIF"
|
||
width="440"
|
||
height="1" border="0"></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/dbSTS/index.html">dbSTS</a> - Database of
|
||
Sequence Tagged Sites - short (about 200-500 bp) genomic sequences that are
|
||
thought
|
||
to be operationally unique in a genome, and therefore define a specific position
|
||
on
|
||
the physical map.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/unists/">UniSTS</a> - a unified,
|
||
non-redundant view of sequence tagged sites (STSs). UniSTS integrates marker
|
||
and
|
||
mapping data from a variety of public resources. If two or more markers have
|
||
different names but the same primer pair, a single STS record is presented for
|
||
the
|
||
primer pair and all the marker names are shown. Each UniSTS record displays the
|
||
primer sequences, product size, mapping information, and cross references to
|
||
Entrez Gene, dbSNP, RHdb, GDB, MGD, and the Map Viewer. The marker report also
|
||
lists
|
||
GenBank and RefSeq records that contain the primer sequences, as determined by
|
||
<a
|
||
href="#ePCR">Electronic PCR (e-PCR)</a>. Data sources include dbSTS, RHdb, GDB,
|
||
various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH
|
||
map,
|
||
Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX
|
||
physical
|
||
map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson
|
||
laboratory's
|
||
MGD map).</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/STS/">e-PCR (Electronic PCR)</a> - find
|
||
putative
|
||
map location of a query sequence. Computational procedure for finding sequence
|
||
tagged sites in DNA sequences. (See <a
|
||
href="#ePCR">additional information</a> in the Tools/Nucleotide Sequence Analysis
|
||
Section.)</ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genemap/">GeneMap'99</a> - physical map of
|
||
>35,000 human gene-based markers, constructed by the International Radiation
|
||
Hybrid
|
||
Mapping Consortium using a consistent set of RH reagents and methodologies.
|
||
Provides a framework for accelerated sequencing efforts by highlighting key
|
||
landmarks (gene-rich regions) of the chromosomes, and represents the cooperative
|
||
efforts of more than one hundred scientists throughout the world.<br>
|
||
<font size="-1"><i>Note:</i> The GeneMap'99 data have also been included in the
|
||
<a
|
||
href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>, described <a
|
||
href="#EntrezMapViewer">above</a>. When viewing a chromosome, use the "Maps &
|
||
Options" dialog box to select the map(s) of interest.</font></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/mapview/static/MVstart.html">Map Viewer</a> -
|
||
graphical views of <a href="/mapview/static/humansearch.html#ObjectTypeSTS">STS
|
||
markers placed on a variety of maps</a>, including sequence, genetic linkage,
|
||
and
|
||
radiation hybrid maps. (See additional information about Map Viewer, <a
|
||
href="#HumanChromosomeMapViews">above</a>.)</ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Omim/getmap.cgi?">Rl2pl4tg
|
||
</a> -
|
||
cytogenetic locations of genes that have been reported in the literature and
|
||
determined by a variety of mapping methods. Can be searched by gene symbol or
|
||
cytogenetic chromosomal location. Accessible from the OMIM page (see Genes,
|
||
above).<br>
|
||
<font size="-1"><i>Note:</i> The OMIM Gene Map data have also been included in
|
||
the
|
||
<a href="/mapview/static/humansearch.html#Genes_Cytogenetic">Genes_Cytogenetic
|
||
Map</a> of the <a href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>
|
||
(described <a href="#EntrezMapViewer">above</a>). When viewing a chromosome,
|
||
use
|
||
the "Maps & Options" dialog box to select the map(s) of
|
||
interest.</font></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: CYTOGENETICS======== -->
|
||
|
||
<a NAME="HumanCytogenetics"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Cytogenetics</FONT><img SRC="spacer10.GIF"
|
||
width="440"
|
||
height="1" border="0"></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/cyto/hbrc.shtml">Human BAC
|
||
Resource</a> -
|
||
A cytogenetic resource of large-insert,
|
||
FISH-mapped clones containing sequence-tagged sites. Will help
|
||
integrate cytogenetic, radiation-hybrid, linkage, and sequence maps of
|
||
the human genome. Includes links to clone distributors.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="/entrez/query.fcgi?db=cancerchromosomes">Cancer
|
||
Chromosomes</a> - An Entrez database that integrates data from three sources:
|
||
the <a
|
||
href="/sky/">NCI/NCBI SKY/M-FISH & CGH Database</a>, the NCI <a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/Mitelman/">Mitelman Database of
|
||
Chromosome
|
||
Aberrations in Cancer</a>, and the NCI <a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/RecurrentAberrations/">Recurrent
|
||
Aberrations in Cancer</a>. Provides the ability to search for cytogenetic,
|
||
clinical, and/or reference information.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SKY_CGH"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/sky/">SKY/M-FISH & CGH Database</a> - The NCI
|
||
and
|
||
NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from
|
||
Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization
|
||
(M-FISH),
|
||
and Comparative Genomic Hybridization (CGH),
|
||
which are complementary fluorescent molecular cytogenetic techniques.
|
||
SKY/M-FISH permits the simultaneous visualization of each human
|
||
or mouse chromosome in a different color, facilitating the identification of
|
||
chromosomal aberrations; CGH can
|
||
be used to generate a map of DNA copy number changes in tumor genomes.
|
||
Collaborative
|
||
project with the National Cancer Institute. (<a
|
||
href="http://www.ncbi.nlm.nih.gov/sky/ccap_helper.cgi?tsc=0">data
|
||
submission instructions...</a>)</ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/Mitelman">Mitelman Database of
|
||
Chromosome
|
||
Aberrations in Cancer</a> - genome-wide map of chromosomal breakpoints in human
|
||
cancer, by Drs. Mitelman, Mertens, and Johansson (eds),
|
||
http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with
|
||
the
|
||
<a href="/CGAP/">Cancer Genome Anatomy Project (CGAP)</a>. <!-- Original
|
||
version of
|
||
the aberration summary was published in a special issue of Nature Genetics, Vol.
|
||
15(Spec. No.):417-74 (April 1997). --><br>
|
||
<font size="-1"><i>Note:</i> The Mitelman data have also been included in the <a
|
||
href="/mapview/map_search.cgi?taxid=9606">Map Viewer</a>, described <a
|
||
href="#EntrezMapViewer">above</a>. When viewing a chromosome, use the "Maps &
|
||
Options" dialog box to select the map(s) of interest.</font></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: GENE EXPRESSION======== -->
|
||
|
||
<a NAME="HumanGeneExpression"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Gene Expression</FONT><img SRC="spacer10.GIF"
|
||
width="440"
|
||
height="1" border="0"></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GEO"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/geo/">Gene Expression Omnibus (GEO)</a> - a
|
||
gene
|
||
expression and hybridization array data repository, as well as a curated, online
|
||
resource for gene expression data browsing, query and retrieval. GEO was the
|
||
first
|
||
fully public high-throughput gene expression data repository, and became
|
||
operational
|
||
in July 2000. Many types of gene expression data from platforms such as spotted
|
||
microarray (microarray), high-density oligonucleotide array (HDA), hybridization
|
||
filter (filter) and serial analysis of gene expression (SAGE) data, are
|
||
accepted,
|
||
accessioned, and archived as a public data set. GEO data can be accessed
|
||
through
|
||
several search and browsing tools on the <a href="/geo/">GEO home page</a>, <a
|
||
href="/Entrez/">Entrez</a> (via <a href="/entrez/query.fcgi?db=geo">Entrez GEO
|
||
Profiles</a> and <a href="/entrez/query.fcgi?db=gds">Entrez GDS (GEO
|
||
DataSets)</a>),
|
||
and the <a href="ftp://ftp.ncbi.nih.gov/pub/geo/">FTP site</a>. The Tools/Gene
|
||
Expression section of this file provides information about <a
|
||
href="#GeneExpressionTools">data visualization and exploration capabilities</a>
|
||
available in GEO.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/ncicgap/">CGAP</a> - Cancer Genome Anatomy
|
||
Project - interdisciplinary program to identify the human genes expressed in
|
||
different cancerous states, based on cDNA (EST) libraries, and to determine the
|
||
molecular profiles of normal, precancerous, and malignant cells. Collaboration
|
||
among the National Cancer Institute, the NCBI, and numerous research labs.
|
||
Additional information about CGAP is provided in the <a
|
||
href="#GeneExpressionTools">Tools/Gene Expression</a> section of this file.
|
||
Related
|
||
resources are described in the <a href="#CancerResearch">Human Genome/Cancer
|
||
Research</a> section.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/SAGE/">SAGEmap</a> - Serial Analysis of Gene
|
||
Expression, or SAGE, is an experimental technique designed to quantitatively
|
||
measure
|
||
gene expression. SAGEmap is an online tool to compare computed gene expression
|
||
profiles between SAGE libraries generated by the Cancer Genome Anatomy Project
|
||
(<b>CGAP</b>, <a href="#CGAP">described</a> under <a
|
||
href="#CancerResearch">human
|
||
genome/cancer research</a>) and submitted by others through the Gene Expression
|
||
Omnibus (<b>GEO</b>, <a href="#GEO">described</a> under <a
|
||
href="#Expression">molecular databases/gene expression</a>). SAGEmap also
|
||
includes a
|
||
comprehensive analysis of SAGE tags in human GenBank records, in which a UniGene
|
||
identifier is assigned to each human sequence that contains a SAGE tag. Data can
|
||
be
|
||
retrieved by tag, by sequence, by UniGene cluster ID and by library name. When
|
||
retrieving data by sequence or UniGene cluster ID, follow a SAGE tag's hotlink
|
||
to
|
||
find out its expression level in different SAGE libraries, and how it is
|
||
represented
|
||
in the rest of the sequences in GenBank. Retrieving data by library name takes
|
||
one
|
||
to GEO, where all SAGEmap data has been stored by library. Analytical tools
|
||
include
|
||
<a href="/SAGE/index.cgi?cmd=expsetup">xProfiler</a>, which compares gene
|
||
expression
|
||
between SAGE libraries of your choice as well as uploaded data. More
|
||
information
|
||
about the additional analytical capabilities of the SAGEmap resource is provided
|
||
in
|
||
the <a href="#GeneExpressionTools">tools/gene expression</a> section of this
|
||
file.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/UniGene/ddd.cgi?ORG=Hs">UniGene DDD</a> -
|
||
Digital
|
||
Differential Display - an online tool to compare computed gene expression
|
||
profiles
|
||
between selected cDNA libraries. Using a statistical test, genes whose
|
||
expression
|
||
levels differ significantly from one tissue to the next are identified and shown
|
||
to
|
||
the user. Additional information about UniGene is <a
|
||
href="#UniGene">above</a>.</li></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: GENETIC VARIATION======== -->
|
||
|
||
<a NAME="HumanGeneticVariation"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Genetic Variation</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/SNP/">dbSNP</a> - Database of Single
|
||
Nucleotide
|
||
Polymorphisms - NCBI database of single nucleotide polymorphisms,
|
||
microsatellites,
|
||
and small-scale insertions and deletions. dbSNP contains population-specific
|
||
frequency and genotype data, experimental conditions, molecular context, and
|
||
mapping
|
||
information for both neutral polymorphisms and clinical
|
||
mutations.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=OMIM">OMIM</a> - Online
|
||
Mendelian Inheritance in Man - allelic variants in ~900 (9%) of OMIM records.
|
||
To
|
||
view a list of those OMIM records, use the <a
|
||
href="/entrez/query.fcgi?CMD=Limits&DB=omim">OMIM Limits page in Entrez</a> and
|
||
check the box for "Allelic Variants" under the section titled "Only records
|
||
with."
|
||
(For more information about OMIM, see <a href="#HumanGenes">Genes</a>,
|
||
above.)</ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MutationDatabases"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Omim/allresources.html">Locus Specific
|
||
Mutation
|
||
Databases</a> - links to numerous external mutation databases are provided on
|
||
the
|
||
OMIM allied resources page and from related <a href="#OMIM">OMIM</a> entries.
|
||
When
|
||
an individual OMIM entry contains links to locus-specific mutation databases,
|
||
the
|
||
links are shown under the "LinkOut" header in the blue sidebar. (The LinkOut
|
||
header
|
||
appears only in entries that have links to resources outside of the Entrez
|
||
system.)</ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: DISORDERS======== -->
|
||
|
||
<a NAME="HumanDisorders"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Disorders</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="GenesAndDisease"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="/books/bv.fcgi?rid=gnd">Genes and Disease</a> - introduction to the
|
||
relationship between genetic factors and human disease. Summary information for
|
||
~60 genetic diseases with links to related databases and
|
||
organizations.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/Mitelman">Mitelman Database of
|
||
Chromosome
|
||
Aberrations in Cancer</a> - genome-wide map of chromosomal breakpoints in human
|
||
cancer, by Drs. Mitelman, Mertens, and Johansson (eds),
|
||
http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with
|
||
the
|
||
<a href="/CGAP/">Cancer Genome Anatomy Project (CGAP)</a>. <!-- Original
|
||
version of
|
||
the aberration summary was published in a special issue of Nature Genetics, Vol.
|
||
15(Spec. No.):417-74 (April 1997). --></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=OMIM">OMIM</a> - Online
|
||
Mendelian Inheritance in Man - continuously updated catalog of human genes and
|
||
genetic disorders, with links to associated literature references, sequence
|
||
records,
|
||
maps, and related databases.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Omim/getmorbid.cgi">OMIM Morbid
|
||
Map</a> -
|
||
alphabetical listing of diseases and corresponding cytogenetic map locations,
|
||
with
|
||
links to OMIM entries. Accessible from OMIM page (see Genes).</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: CANCER RESEARCH======== -->
|
||
|
||
<a NAME="CancerResearch"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3">Cancer Research</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CancerChromosomes"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="/entrez/query.fcgi?db=cancerchromosomes">Cancer
|
||
Chromosomes</a> - An Entrez database that integrates data from three sources:
|
||
the <a
|
||
href="/sky/">NCI/NCBI SKY/M-FISH & CGH Database</a>, the NCI <a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/Mitelman/">Mitelman Database of
|
||
Chromosome
|
||
Aberrations in Cancer</a>, and the NCI <a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/RecurrentAberrations/">Recurrent
|
||
Aberrations in Cancer</a>. Provides the ability to search for cytogenetic,
|
||
clinical, and/or reference information.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CCAP"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/CCAP">CCAP</a>
|
||
- Cancer Chromosome Aberration Project - designed to expedite the definition and
|
||
detailed characterization of the distinct chromosomal alterations that are
|
||
associated with malignant transformation. Collaboration among the National
|
||
Cancer
|
||
Institute, the NCBI, and numerous research labs.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CGAP"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/ncicgap/">CGAP</a> - Cancer Genome Anatomy
|
||
Project - interdisciplinary program to identify the human genes expressed in
|
||
different cancerous states, based on cDNA (EST) libraries, and to determine the
|
||
molecular profiles of normal, precancerous, and malignant cells. Collaboration
|
||
among the National Cancer Institute, the NCBI, and numerous research labs.
|
||
Additional information about CGAP is provided in the <a
|
||
href="#GeneExpressionTools">Tools/Gene Expression</a> section of this
|
||
file.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://cgap.nci.nih.gov/Chromosomes/Mitelman">Mitelman Database of
|
||
Chromosome
|
||
Aberrations in Cancer</a> - genome-wide map of chromosomal breakpoints in human
|
||
cancer, by Drs. Mitelman, Mertens, and Johansson (eds),
|
||
http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with
|
||
the
|
||
<a href="/CGAP/">Cancer Genome Anatomy Project (CGAP)</a>. <!-- Original
|
||
version of
|
||
the aberration summary was published in a special issue of Nature Genetics, Vol.
|
||
15(Spec. No.):417-74 (April 1997). --></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/sky/">SKY/M-FISH & CGH Database</a> - The NCI
|
||
and
|
||
NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from
|
||
Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization
|
||
(M-FISH),
|
||
and Comparative Genomic Hybridization (CGH),
|
||
which are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH
|
||
permits the simultaneous visualization of each human
|
||
or mouse chromosome in a different color, facilitating the identification of
|
||
chromosomal aberrations; CGH can
|
||
be used to generate a map of DNA copy number changes in tumor genomes.
|
||
Collaborative
|
||
project with the National Cancer Institute. (<a
|
||
href="http://www.ncbi.nlm.nih.gov/sky/ccap_helper.cgi?tsc=0">data submission instructions...</a>)</ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/SAGE/">SAGE Analysis</a> - differential
|
||
expression of SAGE tags in cancer libraries. (See additional information about
|
||
SAGEmap, <a href="#SAGEmap">below</a>.) </ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<!-- ========HUMAN GENOME SUB-CATEGORY: FTP======== -->
|
||
|
||
<a NAME="HumanGenomeFTP"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3">FTP</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/">Human
|
||
chromosome data</a> - the ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ directory
|
||
contains one folder for each chromosome, which includes genomic contigs (NT_*
|
||
records) built from finished and unfinished sequence data. The contigs are
|
||
available in various formats, described below. The <a
|
||
href="/genome/guide/build.html">contig assembly and annotation process</a> is
|
||
described in a separate document.
|
||
|
||
<table border="0" cellpadding="0">
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.asn</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">ASN.1 format (description <a
|
||
href="#ASN1">above</a>)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.fa.gz</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">FASTA format (description <a
|
||
href="#FASTA">above</a>)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.gbk.gz</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">GenBank flat file format<br>
|
||
(annotations currently include STS markers; known and
|
||
predicted genes will be added in coming months)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.gbs</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">GenBank summary format<br>
|
||
(this format does not contain sequence data, but instead
|
||
contains a "CONTIG" field, showing how the contig is assembled
|
||
from individual GenBank accessions)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
Data from the Map Viewer (described <a
|
||
href="#HumanChromosomeMapViews">above)</a>,
|
||
is available in the <a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/maps/mapview/">ftp://ftp.ncbi.nih
|
||
.gov
|
||
/genomes/H_sapiens/maps/mapview/</a> subdirectory.
|
||
|
||
</ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: MOUSE======== -->
|
||
<a NAME="MouseGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Mouse Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="95%" BGCOLOR="#FFFFFF">
|
||
<blockquote>
|
||
<a href="#MouseGenomeGuide">Guide</a>,
|
||
<a href="#MouseGenomeChromosomes">Chromosomes</a>,
|
||
<a href="#MouseGenomeSequences">Sequences</a>,
|
||
<a href="#MouseGenomeGenes">Genes</a>,
|
||
<a href="#MouseGenomeClones">Clones</a>,
|
||
<a href="#MouseGenomeMaps">Maps and Mapped Markers</a>,
|
||
<a href="#MouseGenomeCytogenetics">Cytogenetics</a>,
|
||
<a href="#MouseGenomeBLAST">BLAST</a>,
|
||
<a href="#MouseGenomeFTP">FTP</a>
|
||
</td>
|
||
<td CLASS="TEXT" WIDTH="5%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: GUIDE======== -->
|
||
|
||
<a NAME="MouseGenomeGuide"></a>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Guide</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/guide/mouse/">Mouse Genome Resources
|
||
Guide</a> - brings together information on diverse mouse-related resources from
|
||
multiple centers: sequence, mapping, and clone information as well as pointers
|
||
to
|
||
strain and mutant resources.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: CHROMOSOMES======== -->
|
||
|
||
<a NAME="MouseGenomeChromosomes"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Chromosomes</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MouseGenomeSequencing"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/seq/MmHome.html">Mouse Genome
|
||
Sequencing</a> - sequencing progress of the Mouse Genome Project;
|
||
high-throughput
|
||
genomic sequence contigs assembled from finished (phase 3) data; view by
|
||
chromosome
|
||
number, size and physical position; download sequence data by contig or by
|
||
chromosome; BLAST against contigs.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MapViewerMouse"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/mapview/map_search.cgi?taxid=10090">Map
|
||
Viewer</a> - <b>integrated chromosome maps</b> - The Map Viewer is a software
|
||
component of Entrez Genome that displays one or more maps which have been
|
||
aligned
|
||
to each other based on shared marker and gene names,
|
||
and, for the sequence maps, based on a common sequence coordinate system.
|
||
The maps that are currently available for <i>Mus musculus</i> are described in
|
||
the
|
||
<a href="/mapview/static/mousesearch.html"><i>Mus musculus</i> data and search
|
||
tips</a> document. The <a href="/mapview/static/MapViewerHelp.html">Map Viewer
|
||
help
|
||
document</a> provides general information on how to use that
|
||
tool.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: SEQUENCES======== -->
|
||
|
||
<a NAME="MouseGenomeSequences"></a>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Sequences</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/seq/MmHome.html">Mouse Genome
|
||
Sequencing</a> - sequencing progress of the Mouse Genome Project;
|
||
high-throughput
|
||
genomic sequence contigs assembled from finished (phase 3) data; view by
|
||
chromosome
|
||
number, size and physical position; download sequence data by contig or by
|
||
chromosome; BLAST against contigs.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Entrez/">Entrez</a> - includes sequence data
|
||
from
|
||
>160,000 species; use the organism field to limit searches to mouse records.
|
||
See additional information about Entrez <a href="#Entrez">above</a>, and Batch
|
||
Entrez, <a href="#BatchEntrez">below</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: GENES======== -->
|
||
|
||
<a NAME="MouseGenomeGenes"></a>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Genes</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> -
|
||
a gene-based view of the data from a wide range of genomes, including mouse. It
|
||
supplies key connections in the nexus of map, sequence, expression, structure,
|
||
functional, and homology data. <a href="#EntrezGene">More information about
|
||
Entrez Gene</a> is provided above, in the Molecular Databases/Genes section.
|
||
</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/UniGene/Mm.Home.html">UniGene</a> - ESTs and
|
||
full-length mRNA sequences organized into clusters that each represent a unique
|
||
known or putative gene within the organism from which the sequences were
|
||
obtained.
|
||
Additional information about UniGene is provided <a
|
||
href="#UniGene">above</a><!--
|
||
(in both the "<a href="#Nucleotides">Nucleotide Sequences</a>" and "<a
|
||
href="#Genomes">Genomes and Maps</a>/<a href="#MultipleOrganisms">Organism
|
||
Collections</a>" sections) -->.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/HomoloGene/">HomoloGene</a> - a gene homology
|
||
tool that compares nucleotide sequences between pairs of organisms, including
|
||
human,
|
||
mouse, rat, zebrafish, and fruit fly, in order to identify putative orthologs.
|
||
Curated orthologs are incorporated from a variety of sources via
|
||
Entrez Gene.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: CLONES======== -->
|
||
|
||
<a NAME="MouseGenomeClones"></a>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Clones</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/clone/">CloneRegistry</a> - a database
|
||
used by participating <a href="/genome/seq/HsCenters.html">human genome
|
||
sequencing
|
||
centers</a> and <a href="/genome/seq/MmSeqCenters.html">mouse genome sequencing
|
||
centers</a> to record which clones have been selected for sequencing, which are
|
||
currently in the pipeline, and which are finished and represented by sequence
|
||
entries in GenBank. Includes BACs, PACs, cosmids, fosmids. Uses <a
|
||
href="/genome/clone/nomenclature.shtml">standardized clone names</a> that
|
||
represents
|
||
a clone's microtitre plate address (plate number, row, and column) prefixed by a
|
||
library abbreviation, to produce unique names. Includes <a
|
||
href="/genome/clone/ordering.html">clone ordering
|
||
information</a>.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="http://mgc.nci.nih.gov/">Mammalian Gene
|
||
Collection
|
||
(MGC)</a> - The NIH Mammalian Gene Collection (MGC) is a trans-NIH initiative
|
||
that
|
||
seeks to identify and sequence a representative full open reading frame (FL-ORF)
|
||
clone for each human, mouse, and rat gene. Additional information is provided
|
||
<a
|
||
href="#MGC">above</a>.</li></ul></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<a NAME="MouseGenomeCloneFinder"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="/genome/clone/clonefinder/CloneFinder.html">CloneFinder</a> - allow users
|
||
to
|
||
identify clones that contain an object, or that are contained within a
|
||
particular
|
||
genomic region. Clone placement is based on the alignment of BAC end sequences
|
||
(BES)
|
||
to the current genome assembly. Currently, CloneFinder is available for mouse
|
||
only.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: MAPS======== -->
|
||
|
||
<a NAME="MouseGenomeMaps"></a>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Maps and Mapped Markers</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MapViewerMouse"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/mapview/map_search.cgi?taxid=10090">Map
|
||
Viewer</a> - <b>integrated chromosome maps</b> - The Map Viewer is a software
|
||
component of Entrez Genome that displays one or more maps which have been
|
||
aligned
|
||
to each other based on shared marker and gene names,
|
||
and, for the sequence maps, based on a common sequence coordinate system.
|
||
The maps that are currently available for <i>Mus musculus</i> are described in
|
||
the
|
||
<a href="/mapview/static/mousesearch.html"><i>Mus musculus</i> data and search
|
||
tips</a> document. The <a href="/mapview/static/MapViewerHelp.html">Map Viewer
|
||
help
|
||
document</a> provides general information on how to use that
|
||
tool.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/Homology/">Human-Mouse Homology Maps</a> - a
|
||
table comparing genes in homologous segments of DNA from human and mouse, sorted
|
||
by
|
||
position in each genome. Computed by integrating orthologs identified at The
|
||
Jackson Laboratory with putative orthologs identified by sequence homology.
|
||
The <a href="/Homology/Davis/">original maps</a> by M. F. Seldin
|
||
of the University of California at Davis are also available.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/unists/">UniSTS</a> - a unified,
|
||
non-redundant view of sequence tagged sites (STSs). UniSTS integrates marker
|
||
and
|
||
mapping data from a variety of public resources. If two or more markers have
|
||
different names but the same primer pair, a single STS record is presented for
|
||
the
|
||
primer pair and all the marker names are shown. Each UniSTS record displays the
|
||
primer sequences, product size, mapping information, and cross references to
|
||
Entrez Gene, dbSNP, RHdb, GDB, MGD, and the Map Viewer. The marker report also
|
||
lists
|
||
GenBank and RefSeq records that contain the primer sequences, as determined by
|
||
<a
|
||
href="#ePCR">Electronic PCR (e-PCR)</a>. Data sources include dbSTS, RHdb, GDB,
|
||
various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH
|
||
map,
|
||
Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX
|
||
physical
|
||
map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson
|
||
laboratory's
|
||
MGD map).</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: CYTOGENETICS======== -->
|
||
|
||
<a NAME="MouseGenomeCytogenetics"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">Cytogenetics</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/sky/">SKY/M-FISH & CGH Database</a> - The NCI
|
||
and
|
||
NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from
|
||
Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization
|
||
(M-FISH),
|
||
and Comparative Genomic Hybridization (CGH),
|
||
which are complementary fluorescent molecular cytogenetic techniques.
|
||
SKY/M-FISH permits the simultaneous visualization of each human
|
||
or mouse chromosome in a different color, facilitating the identification of
|
||
chromosomal aberrations; CGH can
|
||
be used to generate a map of DNA copy number changes in tumor genomes.
|
||
Collaborative
|
||
project with the National Cancer Institute. (<a
|
||
href="http://www.ncbi.nlm.nih.gov/sky/ccap_helper.cgi?tsc=0">data
|
||
submission instructions...</a>)</ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: BLAST======== -->
|
||
|
||
<a NAME="MouseGenomeBLAST"></a>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3" WIDTH="95%">BLAST</FONT></td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/seq/MmBlast.html">BLAST against the
|
||
mouse
|
||
genome</a> - Nucleotide or protein query sequences can be used. A <a
|
||
href="/genome/seq/Database.html">variety of database choices</a> are provided.
|
||
</ul></td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/BLAST/">BLAST against mouse ESTs</a> -
|
||
compare a
|
||
nucleotide or protein sequence against the human ESTs by choosing
|
||
<b>est_mouse</b>
|
||
as the database to be searched when using Nucleotide BLAST or Translated
|
||
BLAST</ul></td>
|
||
</tr -->
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========MOUSE GENOME SUB-CATEGORY: FTP======== -->
|
||
|
||
<a NAME="MouseGenomeFTP"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3">FTP</td>
|
||
<td WIDTH="5%" BGCOLOR="#FFFFFF" VALIGN="top">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/M_musculus/">Mouse
|
||
chromosome data</a> - the ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ directory
|
||
contains one folder for each chromosome, which includes genomic contigs (NT_*
|
||
records) built from finished sequence data. The contigs are available in
|
||
various
|
||
formats: <!-- The <a href="/genome/guide/build.html">contig assembly and
|
||
annotation
|
||
process</a> is described in a separate document. -->
|
||
|
||
<table border="0" cellpadding="0">
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">mm_chr*.asn</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">ASN.1 format (description <a
|
||
href="#ASN1">above</a>)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">mm_chr*.fa.gz</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">FASTA format (description <a
|
||
href="#FASTA">above</a>)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">mm_chr*.gbk.gz</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">GenBank flat file format<br>
|
||
(annotations currently include STS markers; known and
|
||
predicted genes will be added in coming months)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">mm_chr*.gbs</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">GenBank summary format<br>
|
||
(this format does not contain sequence data, but instead
|
||
contains a "CONTIG" field, showing how the contig is assembled
|
||
from individual GenBank accessions)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
See additional information about the genomes FTP directories, <a
|
||
href="#FTP_OtherGenomes">below</a>
|
||
|
||
</ul></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: RAT======== -->
|
||
<a NAME="RatGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Rat Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="RatGenomeGuide"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genome/guide/rat/">Rat Genome Resources Guide</a> -
|
||
brings together information on diverse rat-related resources from multiple
|
||
centers:
|
||
sequence, mapping, and clone information as well as pointers to strain and
|
||
mutant
|
||
resources.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MapViewerRat"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/map_search.cgi?taxid=10116">Map Viewer</a> -
|
||
<b>integrated chromosome maps</b> - The Map Viewer is a software component of
|
||
Entrez
|
||
Genomes that displays one or more maps which have been aligned to each other
|
||
based
|
||
on shared marker and gene names,
|
||
and, for the sequence maps, based on a common sequence coordinate system.
|
||
The maps that are currently available for rat are described in the <a
|
||
href="/mapview/static/ratsearch.html"><i>Rattus norvegicus</i> data and search
|
||
tips</a> document. The <a href="/mapview/static/MapViewerHelp.html">Map Viewer
|
||
help
|
||
document</a> provides general information on how to use that tool.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> - a
|
||
gene-based view of the data from a wide range of genomes, including rat. It
|
||
supplies key connections in the nexus of map, sequence, expression, structure,
|
||
functional, and homology data. <a href="#EntrezGene">More information about
|
||
Entrez Gene</a> is provided above, in the Molecular Databases/Genes section.
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genome/seq/RnBlast.html">BLAST against the rat
|
||
genome</a>
|
||
- Nucleotide or protein query sequences can be used. A <a
|
||
href="/genome/seq/Database.html">variety of database choices are provided</a>.
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/Rn.Home.html">UniGene</a> - ESTs and
|
||
full-length
|
||
mRNA sequences organized into clusters that each represent a unique known or
|
||
putative gene within the organism from which the sequences were obtained.
|
||
Additional information about UniGene is provided <a
|
||
href="#UniGene">above</a><!--
|
||
(in both the "<a href="#Nucleotides">Nucleotide Sequences</a>" and "<a
|
||
href="#Genomes">Genomes and Maps</a>/<a href="#MultipleOrganisms">Organism
|
||
Collections</a>" sections) -->.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/HomoloGene/">HomoloGene</a> - a gene homology tool
|
||
that
|
||
compares nucleotide sequences between pairs of organisms, including human,
|
||
mouse,
|
||
rat, zebrafish, and fruit fly, in order to identify putative orthologs. Curated
|
||
orthologs are incorporated from a variety of sources via Entrez Gene.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: COW======== -->
|
||
<a NAME="CowGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Cow Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/Rn.Home.html">UniGene</a> - ESTs and
|
||
full-length
|
||
mRNA sequences organized into clusters that each represent a unique known or
|
||
putative gene within the organism from which the sequences were obtained.
|
||
Additional information about UniGene is provided <a
|
||
href="#UniGene">above</a><!--
|
||
(in both the "<a href="#Nucleotides">Nucleotide Sequences</a>" and "<a
|
||
href="#Genomes">Genomes and Maps</a>/<a href="#MultipleOrganisms">Organism
|
||
Collections</a>" sections) -->.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: ZEBRAFISH======== -->
|
||
<a NAME="ZebrafishGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Zebrafish Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ZebrafishGenomeGuide"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genome/guide/zebrafish/">Zebrafish Genome Resources
|
||
Guide</a> - brings together information on diverse zebrafish-related resources
|
||
from
|
||
multiple centers: sequence, mapping, and clone information as well as pointers
|
||
to
|
||
strain and mutant resources.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> - a
|
||
gene-based view of the data from a wide range of genomes, including zebrafish.
|
||
It supplies key connections in the nexus of map, sequence, expression,
|
||
structure, functional, and homology data. <a href="#EntrezGene">More
|
||
information about Entrez Gene</a> is provided above, in the Molecular
|
||
Databases/Genes section.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/map_search.cgi?taxid=7955">Map Viewer</a> -
|
||
<b>integrated chromosome maps</b> - The Map Viewer is a software component of
|
||
Entrez
|
||
Genomes that displays one or more maps which have been aligned to each other
|
||
based
|
||
on shared marker and gene names,
|
||
and, for the sequence maps, based on a common sequence coordinate system.
|
||
The maps that are currently available for <i>Danio rerio</i> are described in
|
||
the <a
|
||
href="/mapview/static/daniosearch.html"><i>Danio rerio</i> genome data and
|
||
search
|
||
tips</a> document. The <a href="/mapview/static/MapViewerHelp.html">Map Viewer
|
||
help
|
||
document</a> provides general information on how to use that tool.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/Dr.Home.html">UniGene</a> - ESTs and
|
||
full-length
|
||
mRNA sequences organized into clusters that each represent a unique known or
|
||
putative gene within the organism from which the sequences were obtained.
|
||
Additional information about UniGene is provided <a
|
||
href="#UniGene">above</a><!--
|
||
(in both the "<a href="#Nucleotides">Nucleotide Sequences</a>" and "<a
|
||
href="#Genomes">Genomes and Maps</a>/<a href="#MultipleOrganisms">Organism
|
||
Collections</a>" sections) -->.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/HomoloGene/">HomoloGene</a> - a gene homology tool
|
||
that
|
||
compares nucleotide sequences between pairs of organisms, including human,
|
||
mouse,
|
||
rat, zebrafish, and fruit fly, in order to identify putative orthologs. Curated
|
||
orthologs are incorporated from a variety of sources via Entrez Gene.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: DROSOPHILA======== -->
|
||
<a NAME="DrosophilaGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3"><i>Drosophila</i>
|
||
Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/map_search.cgi?taxid=7227"><i>Drosophila
|
||
melanogaster</i> Home Page</a> - provides an overview of available resources for
|
||
that organism, graphically displays all the chromosomes (to scale), and allows
|
||
you
|
||
search both cytogenetic and sequence data across the whole genome through the
|
||
Entrez
|
||
Genomes browser. Entrez Genome presents a unified graphical
|
||
view of maps (genetic and physical) and sequence data for an organism. After
|
||
you
|
||
search for a term such as a gene symbol, it presents a graphic Genome View of
|
||
search
|
||
results, from which you can zoom into progressively more detailed Map Views of
|
||
the
|
||
region of interest, and link to sequence data and associated resources that
|
||
contain
|
||
additional detail.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<a NAME="MapViewerDrosophila"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/map_search.cgi?taxid=7227">Map Viewer</a> -
|
||
<b>integrated chromosome maps</b> - The Map Viewer is a software component of
|
||
Entrez
|
||
Genomes that displays one or more maps which have been aligned to each other
|
||
based
|
||
on shared marker and gene names,
|
||
and, for the sequence maps, based on a common sequence coordinate system.
|
||
The sequence and cytogenetic maps that are currently available for
|
||
<i>Drosophila</i>
|
||
are described in the <a
|
||
href="/mapview/static/drosophilasearch.html"><i>Drosophila
|
||
melanogaster</i> genome data and search tips</a> document. The <a
|
||
href="/mapview/static/MapViewerHelp.html">Map Viewer help document</a> provides
|
||
general information on how to use that tool.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> - a
|
||
gene-based view of the data from a wide range of genomes, including
|
||
<i>Drosophila</i>. It
|
||
supplies key connections in the nexus of map, sequence, expression, structure,
|
||
functional, and homology data. <a href="#EntrezGene">More information about
|
||
Entrez Gene</a> is provided above, in the Molecular Databases/Genes section.
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/HomoloGene/">HomoloGene</a> - a gene homology tool
|
||
that
|
||
compares nucleotide sequences between pairs of organisms, including human,
|
||
mouse,
|
||
rat, zebrafish, and fruit fly, in order to identify putative orthologs. Curated
|
||
orthologs are incorporated from a variety of sources via Entrez Gene.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="DrosophilaGenomeBLAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/BLAST/">BLAST against <i>Drosophila melanogaster</i>
|
||
genome sequence</a>
|
||
<ul>
|
||
<li>select <b><i>Drosophila</i> genome</b> as the target database when using the
|
||
nucleotide BLAST, protein BLAST, or translated BLAST search pages. Or,
|
||
<li>check the box for <i>Drosophila melanogaster</i> in the list of organisms on
|
||
the
|
||
<a href="/cgi-bin/Entrez/genom_table_cgi?organism=euk">BLAST with Eukaryotic
|
||
genomes</a> page.
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/genomes/D_melanogaster/">FTP Site</a> - see
|
||
additional information about the genomes FTP directories, <a
|
||
href="#FTP_OtherGenomes">below</a></td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: NEMATODE======== -->
|
||
<a NAME="NematodeGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Nematode Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/map_search.cgi?taxid=6239"><i>Caenorhabditis
|
||
elegans</i> Home Page</a> - Graphical representation of chromosomes that can be
|
||
viewed in their entirety or explored in progressively greater detail in the
|
||
<b>Map
|
||
Viewer</b> (described <a href="#MapViewer">above</a>). Home page also includes
|
||
links to many related resources, such as sequencing centers, other nematode
|
||
sequencing projects, related databases, etc.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/genomes/C_elegans/">FTP
|
||
Site</a> -
|
||
the chromosome data sets are available for ftp in a variety of formats,
|
||
including
|
||
GenBank, FastA, and ASN.1, and others in the <a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/genomes/C_elegans/">genbank/genomes/C_elega
|
||
ns/<
|
||
/a> directory of the NCBI FTP site (ftp://ftp.ncbi.nih.gov/). An NCBI curated
|
||
version of the data is available in the <a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/C_elegans/">genomes/C_elegans/</a>
|
||
directory.
|
||
(See additional note in the FTP section, <a
|
||
href="#FTP_OtherGenomes">below</a>, about the two different FTP directories)<td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: PLANTS======== -->
|
||
<a NAME="PlantGenomes"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Plant Genomes</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/PLANTS/PlantList.html">Plant Genomes
|
||
Central</a>
|
||
- provides access to data from large-scale sequencing projects, genetic maps,
|
||
and
|
||
large-scale EST sequencing projects. All organism names on the page are linked
|
||
to
|
||
the corresponding taxonomic information in NCBI's <b>Taxonomy database</b>
|
||
(described <a href="#Taxonomy">above</a>). In addition, organisms listed under
|
||
"large-scale sequencing projects" and "genetic maps" are represented in the
|
||
<b>Map
|
||
Viewer</b> (described <a href="#MapViewer">above</a>). Organisms listed under
|
||
"large-scale EST sequencing projects" are linked to their EST sequences in
|
||
<b>Entrez</b> (described <a href="#Entrez">above</a>).</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/">UniGene</a> - ESTs and full-length mRNA
|
||
sequences organized into clusters that each represent a unique known or putative
|
||
gene within the organism from which the sequences were obtained. Additional
|
||
information about UniGene is provided <a href="#UniGene">above</a><!-- (in both
|
||
the
|
||
"<a href="#Nucleotides">Nucleotide Sequences</a>" and "<a
|
||
href="#Genomes">Genomes
|
||
and Maps</a>/<a href="#MultipleOrganisms">Organism Collections</a>" sections)
|
||
-->.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: YEAST======== -->
|
||
<a NAME="YeastGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Yeast Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/map_search.cgi?taxid=4932"><i>Saccharomyces
|
||
cerevisiae</i> Home Page</a> - baker's yeast - graphical representation of
|
||
chromosomes that can be viewed in their entirety or explored in progressively
|
||
greater detail in <b>Entrez Genome</b> (described <a
|
||
href="#EntrezGenome">above</a>), with links to associated sequence data. Home
|
||
page
|
||
also includes links to many related resources, such as sequencing centers, other
|
||
fungi sequencing projects, related databases, etc.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/mapview/map_search.cgi?taxid=4896"><i>Schizosaccharomyces
|
||
pombe</i> Home Page</a> - fission yeast - similar to the home page for
|
||
<i>Saccharomyces cerevisiae</i>, described above.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/COG/">COGs - Clusters of Orthologous Groups</a> -
|
||
natural
|
||
system of gene families from complete genomes. Clusters of Orthologous Groups
|
||
(COGs) were delineated by comparing protein sequences encoded in complete
|
||
unicellular genomes representing 30 major phylogenetic lineages. Each COG
|
||
consists
|
||
of individual proteins or groups of paralogs from at least 3 lineages and thus
|
||
corresponds to an ancient conserved domain. The <a href="/COG/old/">Initial
|
||
Version</a> of COGs includes 44 organisms. The <a href="/COG/new/">Updated
|
||
Version</a> of COGs includes 66 organisms in the <a
|
||
href="/COG/new/release/phylox.cgi">Unicellular Clusters</a>, plus <a
|
||
href="/COG/new/shokog.cgi">Eukaryotic Clusters</a> (called KOGs). More
|
||
organisms
|
||
will be added in the future.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="YeastGenomeBLAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/BLAST/">BLAST against the <i>Saccharomyces
|
||
cerevisiae</i>
|
||
or <i>Schizosaccharomyces pombe</i> genome sequences</a>
|
||
<ul>
|
||
<li>check the box for <i>Saccharomyces cerevisiae</i> and/or
|
||
<i>Schizosaccharomyces
|
||
pombe</i> in the list of organisms on the <a
|
||
href="/cgi-bin/Entrez/genom_table_cgi?organism=euk">BLAST with Eukaryotic
|
||
genomes</a> page. OR
|
||
<li>select <b>yeast</b> as the target database when using the nucleotide BLAST,
|
||
protein BLAST, or translated BLAST search pages; this searches only
|
||
<i>Saccharomyces
|
||
cerevisiae</i> data, however.
|
||
</ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/genomes/S_cerevisiae/">FTP
|
||
<i>Saccharomyces cerevisiae</i> Chromosomes</a></td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: MALARIA======== -->
|
||
<a NAME="MalariaGenome"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Malaria Genome</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/projects/Malaria/">Malaria Genetics & Genomics</a> -
|
||
provides data and information relevant to malaria genetics and genomics.
|
||
Resources
|
||
include organism specific sequence BLAST databases (<i>Plasmodium falciparum</i>
|
||
only, all <i>Plasmodium</i>, and all <i>Toxoplasma</i>), genome maps, linkage
|
||
markers, and information about genetic studies. Links are provided for other
|
||
malaria
|
||
web sites and genetic data on related apicomplexan parasites, including
|
||
Toxoplasma
|
||
gondii.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="mapview">Map Viewer</a> - The Map Viewer (described <a
|
||
href="#MapViewer">above</a>) provides graphical views and search capabilities
|
||
for
|
||
both <a href="/mapview/map_search.cgi?taxid=5833"><i>Plasmodium
|
||
falciparum</i></a>
|
||
and <a href="/mapview/map_search.cgi?taxid=7165"><i>Anopheles gambiae</i>
|
||
(malaria
|
||
mosquito)</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MalariaGenomeBLAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/projects/Malaria/blastindex.html">BLAST against
|
||
Malaria
|
||
sequences</a>
|
||
<ul>
|
||
<li>The malaria genome sequence (both <i>Plasmodium yoelii</i> shotgun
|
||
sequences and <i>Plasmodium falciparum</i> complete finished sequence)
|
||
as submitted to GenBank is available at the <a
|
||
href="/BLAST/Genome/plasmodium.html">Entrez
|
||
Genome Malaria BLAST</a> page.</li>
|
||
<li>Prior release and unsubmitted sequence
|
||
data to GenBank is available from the <a
|
||
href="/projects/Malaria/plasmodiumblcus.html">NCBI
|
||
Malaria Genetics & Genomics Custom BLAST</a> page.</li>
|
||
<!-- old wording: li><a href="/projects/Malaria/plasmodiumblcus.html">Custom
|
||
BLAST</a> provides access to unfinished sequences "pulled" from the respective
|
||
P.
|
||
falciparum 3D7 Genome Sequencing Center's FTP sites: Sanger Centre, Stanford,
|
||
and
|
||
TIGR or the Gene Sequencing Tag Project at the Univ of Florida. </li -->
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/Plasmodium_falciparum/">FTP</a>
|
||
<ul>
|
||
<li><a href="ftp://ftp.ncbi.nih.gov/pub/Malaria/">Electronic PCR (e-PCR)
|
||
program
|
||
for finding STSs in DNA sequences, Malaria Packaging Version</a> - Standalone
|
||
Program. (See <a
|
||
href="#ePCR">additional information</a> in the Tools/Nucleotide Sequence Analysis
|
||
Section.)</li>
|
||
<li><a href="ftp://ftp.ncbi.nih.gov/genomes/Plasmodium_falciparum/">download
|
||
completed chromosome sequence data</a></li>
|
||
<!-- old: li><a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/genomes/P_falciparum/">download sequence
|
||
data
|
||
from completed chromosomes</a> (currently chromosomes 2 and 3) in a variety of
|
||
formats, including GenBank flat file (*.gbk), GenBank summary file (*.gbs),
|
||
FASTA
|
||
Nucleic Acid file (*.fna), FASTA Amino Acid file (*.faa), Protein Table (*.ptt),
|
||
and
|
||
others.</li -->
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: MICROBIAL GENOMES======== -->
|
||
<a NAME="MicrobialGenomes"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Microbial Genomes</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=Genome">Entrez Genome</a> -
|
||
Graphical representation of complete bacterial genomes that can be viewed in
|
||
their
|
||
entirety or explored in progressively greater detail; links to associated
|
||
sequence
|
||
data. A "ProtTable" of protein coding genes is provided for each bacterium.
|
||
There
|
||
are also links to a "TaxTable," showing the distribution of BLAST protein
|
||
homologs
|
||
by taxa (sequences grouped by superkingdom), and to a distribution of BLAST
|
||
protein
|
||
homologs by 3-D structure (sequences with known structure). Additional
|
||
information
|
||
about Entrez Genome is also provided <a href="#EntrezGenome">above</a>.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?DB=genomeprj">Entrez Genome
|
||
Project</a> -
|
||
provides an umbrella view of the status of a wide range of genome projects,
|
||
and includes information about <a href="/genomes/MICROBES/microbial_taxtree.html">microbial
|
||
genome sequencing projects</a>. Tabs allow you to switch between lists of
|
||
completed
|
||
and in-progress microbial genome projects. The list of completed genomes
|
||
includes
|
||
links to NCBI graphical views of the data (in Entrez Genome), sequencing
|
||
centers, and
|
||
the results of various analyses that have been done on the genomes at NCBI
|
||
(e.g., TaxTable, COG Table,
|
||
3-D Neighbors, and more). The list of in-progress sequencing projects includes
|
||
links
|
||
to sequencing centers and, when available, to BLASTable data. A
|
||
<a href="#EntrezGenomeProject">more detailed description of the Entrez Genome
|
||
Project
|
||
database</a> is provided in the section on <a href="#Genomes">Genomes and
|
||
Maps/Organism Collections</a>.
|
||
</td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/COG/">COGs - Clusters of Orthologous Groups</a> -
|
||
natural
|
||
system of gene families from complete genomes. Clusters of Orthologous Groups
|
||
(COGs) were delineated by comparing protein sequences encoded in complete
|
||
unicellular genomes representing 30 major phylogenetic lineages. Each COG
|
||
consists
|
||
of individual proteins or groups of paralogs from at least 3 lineages and thus
|
||
corresponds to an ancient conserved domain. The <a href="/COG/old/">Initial
|
||
Version</a> of COGs includes 44 organisms. The <a href="/COG/new/">Updated
|
||
Version</a> of COGs includes 66 organisms in the <a
|
||
href="/COG/new/release/phylox.cgi">Unicellular Clusters</a>, plus <a
|
||
href="/COG/new/shokog.cgi">Eukaryotic Clusters</a> (called KOGs). More
|
||
organisms
|
||
will be added in the future.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/genom_table.cgi">BLAST against Microbial
|
||
Genomes</a> - sequences from selected completed and unfinished eukaryotic and
|
||
prokaryotic genomes; partial genomic sequences have been graciously provided by
|
||
the
|
||
sequencing centers or extracted from GenBank. NCBI encourages sequencing
|
||
centers to
|
||
submit partially sequenced genomes to be included in this BLAST page. Data can
|
||
be
|
||
submitted via ftp, after contacting genomes@ncbi.nlm.nih.gov to set up an
|
||
account.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT">FTP - download complete bacterial genomes in a variety of
|
||
formats,
|
||
including GenBank flat file (*.gbk), GenBank summary file (*.gbs), FASTA Nucleic
|
||
Acid file (*.fna), FASTA Amino Acid file (*.faa), Protein Table (*.ptt), and
|
||
others.
|
||
<ul>
|
||
<li><a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/">complete
|
||
bacterial
|
||
genomes as submitted to <b>GenBank</b></a>.
|
||
<li><a href="ftp://ftp.ncbi.nih.gov/genomes/Bacteria/">complete bacterial
|
||
genomes
|
||
from the <b>RefSeq</b> database</a> (described <a href="#RefSeq">above</a>).
|
||
</ul>
|
||
<blockquote>(See additional note in the FTP section, <a
|
||
href="#FTP_OtherGenomes">below</a>, about the two different FTP directories)
|
||
</blockquote>
|
||
</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: VIRUSES======== -->
|
||
<a NAME="ViralGenomes"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Viral Genomes</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<a NAME="ViralReferenceSequences"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/VIRUSES/viruses.html">Viruses Home Page</a>
|
||
provides brief background information on the biology of viruses, links to
|
||
viral genome sequences in Entrez Genome (described below), and a wide range of
|
||
related resources. It also includes information about <a
|
||
href="/genomes/VIRUSES/viroabout.html">Viral Reference
|
||
Sequences</a>, a collection of reference sequences for more than 1000 viral
|
||
genomes.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/static/vis.html">Entrez Genome</a> -
|
||
Graphical
|
||
representation of complete viral genomes that can be viewed in their entirety or
|
||
explored in progressively greater detail; links to associated sequence data. A
|
||
summary of Coding Regions (described <a href="#ProtTaxTable">above</a>) is
|
||
provided
|
||
for each virus. Additional information about Entrez Genome is also provided <a
|
||
href="#EntrezGenome">above</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="FluVirus"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/FLU/FLU.html">Influenza Virus Resource</a> -
|
||
A collection of
|
||
resources specifically designed to support the research on the flu virus.
|
||
Includes
|
||
links to genome sequence data, analytical tools, epidemiological information,
|
||
and the
|
||
<a href="http://www.nih.gov/news/pr/nov2004/niaid-15.htm">Influenza Genome
|
||
Sequencing Project</a>, funded by the National Institute of Allergy and
|
||
Infectious Diseases (<a href="http://www.niaid.nih.gov/">NIAID</a>).
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Retroviruses"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/retroviruses/">Retrovirus Resources</a> - A
|
||
collection of
|
||
resources specifically designed to support the research of retroviruses.
|
||
Resources
|
||
include a genotyping tool that uses the BLAST algorithm to identify the genotype
|
||
of
|
||
a query sequence; an alignment tool for global alignment of multiple sequences;
|
||
an
|
||
HIV-1 automatic sequence annotation tool; and annotated maps of 16 retroviruses
|
||
viewable in GenBank, FASTA, and graphic formats, with links to associated
|
||
sequence
|
||
records.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/RefSeq/HIVInteractions/">HIV Interactions</a> - The
|
||
HIV-1, Human Protein Interaction Database contains information about known
|
||
interactions of HIV-1 proteins with proteins from human hosts. It provides
|
||
annotated bibliograhies of published reports of protein interactions, with links
|
||
to
|
||
the corresponding PubMed records and sequence data. <a
|
||
href="#HIVInteractions">More
|
||
information</a> about this database is provided under "Literature Databases".
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PASC"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/pasc/viridty.cgi?textpage=overview">PASC (PAirwise Sequence Comparison)</a> - a web tool for analysis of pairwise identity distribution within viral families. The identities are pre-computed for every pair within the families and with distribution plotted in a form of histogram where each bar corresponds to an interval of identities. Only complete genomes should be used as query sequences. The results from partial sequences are not suitable for the purpose of this tool. After you submit your sequence, PASC will start computing pairwise identities between the external genome and the existing genome sequences of the family. At the end of the process, you will be presented with the list of 15 closest matches to the genome within the family. The <a href="/sutils/pasc/viridty.cgi?textpage=documentation">documentation</a> provides more details about using PASC.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: VIROIDS======== -->
|
||
<a NAME="ViroidGenomes"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Viroid Genomes</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/static/vid.html">Entrez Genome</a> -
|
||
Graphical
|
||
representation of complete viroid genomes with links to corresponding sequence records. Additional information about Entrez Genome is also provided <a
|
||
href="#EntrezGenome">above</a>.</td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: PLASMIDS======== -->
|
||
<a NAME="Plasmids"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Plasmids</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/static/o.html">Entrez Genome</a> - Graphical
|
||
representation of complete plasmids that can be viewed in their entirety or
|
||
explored
|
||
in progressively greater detail; links to associated sequence data. A summary
|
||
of
|
||
Coding Regions (described <a href="#ProtTaxTable">above</a>) is provided for
|
||
each
|
||
plasmid. Additional information about Entrez Genome is also provided <a
|
||
href="#EntrezGenome">above</a>.</td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN GENOMES_AND_MAPS: EUKARYOTIC_ORGANELLES======== -->
|
||
<a NAME="EukaryoticOrganelles"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Eukaryotic
|
||
Organelles</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/ORGANELLES/organelles.html">Eukaryotic
|
||
Organelles
|
||
Home Page</a> - Provides an overview of eukaryotic organelles; a description of
|
||
the Organelle Reference Sequences
|
||
project (part of RefSeq, see <a href="#RefSeq">above</a>); and links to (a)
|
||
lists of
|
||
completely sequenced organelles shown in taxonomic hierarchy and alphabetically
|
||
by
|
||
organism, (b) gene and RNA order in metazoan mitochondria, and (c) related web
|
||
sites.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genomes/static/euk_o.html">Entrez Genome</a> -
|
||
Graphical
|
||
representation of complete eukaryotic organelles that can be viewed in their
|
||
entirety or explored in progressively greater detail; links to associated
|
||
sequence
|
||
data. A summary of Coding Regions (described <a href="#ProtTaxTable">above</a>)
|
||
is
|
||
provided for each organelle. Additional information about Entrez Genome is also
|
||
provided <a href="#EntrezGenome">above</a>.</td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- =========================END_GENOMES_AND_MAPS==================== -->
|
||
|
||
<!-- ===========================TOOLS============================== -->
|
||
<a NAME="Tools"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" CLASS="H3a">Tools</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a
|
||
href="../Tools/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<table BORDER="0" WIDTH="98%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="95%" BGCOLOR="#FFFFFF">
|
||
<blockquote>
|
||
<a href="#Entrez">Text Term Searching (Entrez)</a>,
|
||
<a href="#BLAST">Sequence Similarity Searching (BLAST)</a>,
|
||
<a href="#NucleotideSequenceAnalysis">Nucleotide Sequence Analysis</a>,
|
||
<a href="#ProteinSequenceAnalysis">Protein Sequence Analysis and Proteomics</a>,
|
||
|
||
<a href="#StructureTools">3-D Structure Display and Similarity Searching</a>,
|
||
|
||
<a href="#GenomeAnalysisTools">Genome Analysis</a>,
|
||
<a href="#GeneExpressionTools">Gene Expression</a>
|
||
</td>
|
||
<td CLASS="TEXT" WIDTH="5%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
<br>
|
||
|
||
<!-- ========CATEGORY WITHIN TOOLS: TEXT SEARCHING======== -->
|
||
<a NAME="Entrez"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Data Retrieval - Text Term
|
||
Searching</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Entrez/">Entrez</a> - provides integrated access to
|
||
nucleotide and protein sequence data from >160,000 organisms, along with 3D
|
||
protein
|
||
structures, genomic mapping information, PubMed MEDLINE, and more.Sequence data
|
||
are
|
||
combined from various sources, including GenBank, EMBL, DDBJ, RefSeq,
|
||
PIR-International, PRF, Swiss-Prot, and PDB. A <a
|
||
href="/Database/datamodel/index.html"><b>Data Model</b></a> provides a schematic
|
||
illustration of the connections between the many data types in Entrez.
|
||
|
||
<ul>
|
||
<li><b>Two unique features</b> of Entrez are:</li>
|
||
<ol>
|
||
<li><b>pre-computed similarity searches</b> for each database record,
|
||
identifying the <b>related records ("neighbors")</b> within that database. The
|
||
algorithm used to identify related records depends upon the database.</li>
|
||
<li><b>links</b> from a record in one database to associated records in the
|
||
other Entrez databases, providing <b>integrated access across the various
|
||
databases</b>. For exmaple, if a MEDLINE record cites a GenBank nucleotide
|
||
sequence
|
||
record, which in turn is linked to a protein translation, there will be a link
|
||
between those three records. The <a
|
||
href="/Database/datamodel/index.html"><b>Entrez
|
||
Data Model</b></a> illustrates the links that exist among the various Entrez
|
||
Databases.</li>
|
||
</ol>
|
||
|
||
<li><b>Entrez can be searched</b> with a wide variety of text terms such as
|
||
author
|
||
name, journal name, gene or protein name, organism, unique identifier (e.g.,
|
||
accession number, sequence ID, PubMed ID), and other terms, depending on the
|
||
database being searched.</li>
|
||
|
||
<li>The <a href="/entrez/query/static/help/helpdoc.html"><b>help
|
||
document</b></a>
|
||
provides more information about the databases available in Entrez as well as
|
||
search
|
||
tips. External resources can be linked to Entrez records using the new
|
||
<b>Linkout</b> service (described <a href="#LinkOut">below</a>). Entrez also
|
||
allows
|
||
users to store search strategies and select a customized subset of LinkOut links
|
||
through the NCBI <b>My NCBI</b> service (described <a
|
||
href="#MyNCBI">below</a>).</li>
|
||
</ul>
|
||
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="AdvancedEntrez"></a>
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><b><a href="/entrez/query/static/advancedentrez.html">Advanced
|
||
Entrez Tools</a></b> - A number of additional Entrez tools provide advanced
|
||
searching capabilities (including Batch Entrez, described below); the ability to
|
||
set
|
||
preferences, store search strategies, and select resources for LinkOut
|
||
(described <a
|
||
href="#LinkOut">above</a>) display; and the ability to access Entrez data
|
||
through
|
||
programming tools (including Entrez Utilities, described below).</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<a NAME="BatchEntrez"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><b>Batch Entrez</b> - allows you to retrieve a large number of
|
||
<a
|
||
href="/entrez/batchentrez.cgi?db=Nucleotide">nucleotide sequences</a> or <a
|
||
href="/entrez/batchentrez.cgi?db=Protein">protein sequences</a> from Entrez, in
|
||
a
|
||
batch mode, by importing a file containing a list of the desired <a
|
||
href="samplerecord.html#GInB">GI</a> or <a
|
||
href="samplerecord.html#AccessionB">accession numbers</a>. Search results are
|
||
saved
|
||
directly to a local disk file on your computer.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="EntrezUtilities"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query/static/eutils_help.html">Entrez
|
||
Utilities</a> - Entrez Programming Utilities, also called E-Utilities, are tools
|
||
that provide access to Entrez data outside of the regular web query interface.
|
||
They
|
||
represent a method of <a href="/entrez/query/static/linking.html">making WWW
|
||
links
|
||
to Entrez</a>.
|
||
Each utility performs a specialized retrieval task, and can be used simply by
|
||
writing a specially formatted URL. For example, EFetch retrieves records in the
|
||
requested format from a list of one or more primary IDs or from the user's
|
||
environment. The E-Utilities web page describes the available utilities and
|
||
links
|
||
to a brief help document for each one. E-Utilities can be helpful for
|
||
retrieving
|
||
search results for future use in another environment. To receive announcements
|
||
about about Entrez Utilities, see the <a href="Summary/email_lists.html">NCBI
|
||
Email
|
||
Lists</a> page.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="LinkOut"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/linkout/doc/linkoutoverview.html">LinkOut</a>
|
||
- a
|
||
registry service to create links from specific articles, journals, or biological
|
||
data in Entrez (described <a href="#Entrez">above</a>) to resources on external
|
||
web
|
||
sites. Third parties can provide a URL, resource name, brief description of
|
||
their
|
||
web site, and specification of the NCBI data from which they would like to
|
||
establish
|
||
links. The specification can be written as a valid Boolean query to Entrez, or
|
||
as a
|
||
list of identifiers for specific articles or sequences. Entrez PubMed users can
|
||
then
|
||
select which external links are visible in their searches, through the NCBI
|
||
<b>My NCBI</b> service</a> (described <a href="#MyNCBI">below</a>). To
|
||
receive announcements about updates and new features in LinkOut, see the <a
|
||
href="Summary/email_lists.html">NCBI Announcements Email Lists</a> page.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MyNCBI"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/cubby.fcgi?call=QueryExt.CubbyQuery..Show
|
||
All">My NCBI</a> -
|
||
Formerly known as "Cubby", My NCBI allows Entrez users to store and update
|
||
searches, receive automatic e-mails of search updates, select the Filter folder
|
||
tabs shown by default for any Entrez database, and customize their LinkOut
|
||
(described <a href="#LinkOut">above</a>) display to include or exclude links to
|
||
providers. My NCBI requires that your system accepts <a
|
||
href="/entrez/query/static/faq.html#Acceptscookies">cookies</a>. You must also
|
||
complete a brief registration form in which you select a username and password.
|
||
You will need those in order to access your "My NCBI" account. There is also an
|
||
option to remain logged into My NCBI, if desired. For additional information, see
|
||
the <a
|
||
href="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.My_NCBI">help document</a> and <a
|
||
href="http://www.nlm.nih.gov/pubs/techbull/jf05/jf05_myncbi.html">tutorial</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="QueryEmailServer"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="../Genbank/GenBankEmail.html">Query E-mail Server</a>
|
||
-
|
||
The Query server, which provided e-mail access to a subset of Entrez databases,
|
||
was
|
||
<b>discontinued on April 15, 2002</b> because of limited usage. Almost all
|
||
Entrez
|
||
searchers now use the WWW Entrez interface, described <a
|
||
href="#Entrez">above</a>.
|
||
It provides access to more databases and more features than are possible through
|
||
the
|
||
e-mail interface.</td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><a href="/Entrez/Network/nentrez.overview.html">Network
|
||
Entrez</a>
|
||
- a TCP/IP-based client-server version of WWW Entrez. Makes a direct connection
|
||
with
|
||
the NCBI databases over the Internet to retrieve data. The data comes in a
|
||
binary
|
||
form taking up less network bandwidth for transmittance. Client software is
|
||
available for PC, Mac, and Unix.</td>
|
||
</tr -->
|
||
</table>
|
||
|
||
<a NAME="IRX"></a>
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/irx/dbST/dbest_query.html">dbEST</a>, <a
|
||
href="/dbST/dbgss_query.html">dbGSS</a>, <a
|
||
href="/dbST/dbsts_query.html">dbSTS</a>
|
||
search pages - EST, GSS, and STS sequences are available from two sources: the
|
||
EST/GSS/STS divisions of GenBank (via Entrez), and separate but related
|
||
databases
|
||
called dbEST/dbGSS/dbSTS. The sequences and accession numbers in both sources
|
||
are
|
||
the same but the record formats differ. The search bar at the top of the dbEST
|
||
and
|
||
dbGSS home pages searches the GenBank EST and GSS divisions through Entrez. The
|
||
records are displayed in dbEST/dbGSS format by default, and can be displayed in
|
||
GenBank flat file format, if desired.</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query/static/overview.html#Citation
|
||
Matcher">Citation Matcher</a> - allows you to find the PubMed ID of any article
|
||
in
|
||
the PubMed database, given its bibliographic information (journal, volume, page,
|
||
etc.). </td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/query/static/citmatch.html">Citation
|
||
Matcher for single articles</a></i></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/entrez/getids.cgi">Batch Citation Matcher for
|
||
many articles</a></i></ul></td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><ul><li>E-Mail Citation Matcher is also available, and can be
|
||
used
|
||
for or one or many articles. To obtain the help documentation, send the word
|
||
HELP
|
||
in the body of a message to the server address: <a
|
||
href="mailto:citation_matcher@ncbi.nlm.nih.gov">citation_matcher@ncbi.nlm.nih.go
|
||
v</a
|
||
></i></ul></td>
|
||
</tr -->
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN TOOLS: SEQUENCE SIMILARITY SEARCHING======== -->
|
||
<a NAME="BLAST"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Sequence Similarity Searching</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<br>
|
||
<!-- ======== Top of Border around BLAST home page categories ======== -->
|
||
|
||
<table BGCOLOR="#006699" BORDER="0" CELLSPACING=0 CELLPADDING=3 WIDTH="90%">
|
||
<tr>
|
||
<td CLASS="TEXT">
|
||
<!-- ======== Top of Border around BLAST home page categories ======== -->
|
||
|
||
<table BGCOLOR="#FFFFFF" BORDER="0" CELLSPACING=0 CELLPADDING=5 WIDTH="100%">
|
||
<tr>
|
||
<td CLASS="TEXT" BGCOLOR="#FFFFFF"><a href="/BLAST/">BLAST Home Page</a> -
|
||
provides access to BLAST (Basic Local Alignment Search Tool) programs, overview,
|
||
help documentation, FAQs</a>. BLAST programs include:
|
||
<ul>
|
||
<li>Nucleotide BLAST
|
||
<ul>
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&HITLIST_SIZE=100&NCB
|
||
I_GI
|
||
=on&PAGE=Nucleotides&PROGRAM=blastn&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS
|
||
.y=8
|
||
&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes">Standard nucleotide-nucleotide BLAST
|
||
[blastn]</a> (more about <a href="#BLAST2.x">BLAST 2.x</a> and <a
|
||
href="/blast/html/BLASThomehelp.html#NTBLAST">nucleotide BLAST</a>)
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&HITLIST_SIZE=100&NCB
|
||
I_GI
|
||
=on&PAGE=MegaBlast&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS.y=8&SHOW_OVERVIE
|
||
W=on
|
||
&END_OF_HTTPGET=Yes">MegaBLAST</a> (described <a href="#MegaBLAST">below</a>)
|
||
<ul>
|
||
<li><a href="/blast/mmtrace.html">MegaBLAST against the Trace
|
||
Archives</a>
|
||
(described <a href="#MegaBLAST">below</a>)
|
||
<li><a href="/BLAST/tracemb.shtml">Discontiguous MegaBLAST against the
|
||
Trace
|
||
Archives</a> (described <a href="#MegaBLAST">below</a>)
|
||
</ul>
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=1000&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&HITLIST_SIZE=100&NCBI_GI=on
|
||
&PAG
|
||
E=Nucleotides&PROGRAM=blastn&SERVICE=plain&SET_DEFAULTS.x=29&SET_DEFAULTS.y=6&SH
|
||
OW_O
|
||
VERVIEW=on&WORD_SIZE=7&END_OF_HTTPGET=Yes">Search for short nearly exact
|
||
matches</a>
|
||
(<a href="/blast/html/BLASThomehelp.html#NTBLAST">more...</a>)
|
||
</ul>
|
||
<li>Protein BLAST
|
||
<ul>
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on
|
||
&DAT
|
||
ABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=A
|
||
lign
|
||
ment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Protei
|
||
ns&P
|
||
ROGRAM=blastp&SERVICE=plain&SET_DEFAULTS.x=41&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&
|
||
END_
|
||
OF_HTTPGET=Yes">Standard protein-protein BLAST [blastp]</a> (more about <a
|
||
href="#BLAST2.x">BLAST 2.x</a> and <a
|
||
href="/blast/html/BLASThomehelp.html#AABLAST">protein BLAST</a>)
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=250
|
||
&ALIGNMENT_VIEW=Pairwise&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&
|
||
CDD_
|
||
SEARCH=on&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FORMAT_OBJECT=Alignment
|
||
&FOR
|
||
MAT_TYPE=HTML&HITLIST_SIZE=100&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PA
|
||
GE=P
|
||
roteins&PROGRAM=blastp&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS.x=36&SET_DEFAU
|
||
LTS.
|
||
y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes">PSI-BLAST and PHI-BLAST</a> (described
|
||
<a
|
||
href="#PHI-BLAST">below</a>)
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=20000&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GAPCOSTS=9+1&HITLIST_SIZE=
|
||
100&
|
||
I_THRESH=0.005&MATRIX_NAME=PAM30&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&SERVICE
|
||
=pla
|
||
in&SET_DEFAULTS.x=24&SET_DEFAULTS.y=10&SHOW_OVERVIEW=on&WORD_SIZE=2&END_OF_HTTPG
|
||
ET=Y
|
||
es">Search for short nearly exact matches</a> (<a
|
||
href="/blast/html/BLASThomehelp.html#AABLAST">more...</a>)
|
||
</ul>
|
||
<li>Translated BLAST Searches
|
||
<ul>
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=1&HITLI
|
||
ST_S
|
||
IZE=100&NCBI_GI=on&PAGE=Translations&PROGRAM=blastx&SERVICE=plain&SET_DEFAULTS.x
|
||
=37&
|
||
SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=no&END_OF_HTTPGET=Yes">Nucl
|
||
eoti
|
||
de query - Protein db [blastx]</a> (<a
|
||
href="/blast/html/BLASThomehelp.html#TRBLAST">more...</a>)
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=0&HITLI
|
||
ST_S
|
||
IZE=100&NCBI_GI=on&PAGE=Translations&PROGRAM=tblastn&SERVICE=plain&SET_DEFAULTS.
|
||
x=23
|
||
&SET_DEFAULTS.y=10&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=no&END_OF_HTTPGET=Yes">Pr
|
||
otei
|
||
n query - Translated nucleotide db [tblastn]</a> (<a
|
||
href="/blast/html/BLASThomehelp.html#TRBLAST">more...</a>)
|
||
<li><a
|
||
href="/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=50&
|
||
ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(no
|
||
ne)&
|
||
EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=1&HITLI
|
||
ST_S
|
||
IZE=100&NCBI_GI=on&PAGE=Translations&PROGRAM=tblastx&SERVICE=plain&SET_DEFAULTS.
|
||
x=21
|
||
&SET_DEFAULTS.y=9&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=yes&END_OF_HTTPGET=Yes">Nu
|
||
cleo
|
||
tide query - Translated nucleotide db [tblastx]</a> (<a
|
||
href="/blast/html/BLASThomehelp.html#TRBLAST">more...</a>)
|
||
</ul>
|
||
<li>Search for conserved domains
|
||
<ul>
|
||
<li><a href="/Structure/cdd/wrpsb.cgi">Search the Conserved Domain Database
|
||
using RPS-BLAST</a> (see CD-Search, described <a href="#CD-Search">below</a>)
|
||
<li><a href="/Structure/lexington/lexington.cgi?cmd=rps">Search by domain
|
||
architecture [CDART]</a> (described <a href="#CDART">below</a>)
|
||
</ul>
|
||
<li>Pairwise BLAST
|
||
<ul>
|
||
<li><a href="/blast/bl2seq/bl2.html">BLAST 2 Sequences</a> (described <a
|
||
href="#BLAST2Sequences">below</a>)
|
||
</ul>
|
||
|
||
<li>Genomic BLAST pages
|
||
<ul>
|
||
|
||
<li>Mammals</li>
|
||
<ul>
|
||
<li><a href="/genome/seq/HsBlast.html">Human Genome</a> (additional
|
||
information <a href="#HumanGenomeBLAST">above</a>)</li>
|
||
|
||
<li><a href="/genome/seq/MmBlast.html">Mouse Genome</a> (additional
|
||
information <a href="#MouseGenomeBLAST">above</a>)</li>
|
||
|
||
<li><a href="/genome/seq/RnBlast.html">Rat Genome</a> (additional
|
||
information <a href="#RatGenomeBLAST">above</a>)</li>
|
||
|
||
<li><a href="/genome/seq/BtaBlast.html">Cow Genome</a> (additional
|
||
information <a href="#RatGenomeBLAST">above</a>)</li>
|
||
|
||
<li><a href="/genome/seq/SscBlast.html">Pig Genome</a> (additional
|
||
information <a href="#RatGenomeBLAST">above</a>)</li>
|
||
|
||
<li><a href="/genome/seq/CfaBlast.html">Dog Genome</a> (additional
|
||
information <a href="#RatGenomeBLAST">above</a>)</li>
|
||
</ul>
|
||
|
||
<li>Other Vertebrates</li>
|
||
<ul>
|
||
<li><a href="/genome/seq/DrBlast.html">Zebrafish Genome</a></li>
|
||
<li><a href="/BLAST/Genome/fugu.html"><i>Fugu rubripes</i>
|
||
Genome</a></li>
|
||
</ul>
|
||
|
||
<li>Invertebrates</li>
|
||
<ul>
|
||
<li><a href="/BLAST/Genome/Insects.html"><i>Drosophila
|
||
melanogaster</i></a></li>
|
||
<li><a href="/BLAST/Genome/Insects.html"><i>Anopheles
|
||
gambiae</i></a></li>
|
||
</ul>
|
||
|
||
<li>Nematodes</li>
|
||
<ul>
|
||
<li><a href="/BLAST/Genome/NematodeBlast.html"><i>Caenorhabditis
|
||
elegans</i></a></li>
|
||
</ul>
|
||
|
||
<li><a href="/BLAST/Genome/PlantBlast.shtml">Plants</a></li>
|
||
|
||
<li><a href="/BLAST/Genome/FungiBlast.html">Fungi</a></li>
|
||
<!-- ul>
|
||
<li><a href="/BLAST/Genome/FungiBlast.html"><i>Saccharomyces
|
||
cerevisiae</i></a></li>
|
||
<li><a href="/BLAST/Genome/FungiBlast.html"><i>Schizoaccharomyces
|
||
pombe</i></a></li>
|
||
<li><a href="/BLAST/Genome/FungiBlast.html"><i>Neurospora
|
||
crassa</i></a></li>
|
||
<li><a href="/BLAST/Genome/FungiBlast.html"><i>Magnaporthe
|
||
grisea</i></a></li>
|
||
</ul -->
|
||
|
||
<li>Protozoa</li>
|
||
<ul>
|
||
<li><a href="/BLAST/Genome/plasmodium.html"><i>Plasmodium
|
||
falciparum</i></a>
|
||
(malaria)</li>
|
||
</ul>
|
||
|
||
<li><a href="/sutils/genom_tree.cgi?organism=euk">Other Eukaryotic
|
||
Genomes</a></li>
|
||
|
||
<li><a href="/sutils/genom_table.cgi">Bacteria</a></li>
|
||
|
||
<li><a href="/ORGANELLES/mblast.cgi?gene=COX1&tax=33208">Organelles</a></li>
|
||
|
||
<li><a
|
||
href="/GENOMES/Bitor.cgi?db=VOG&data=vog&gdata=dsdna.defl">Viruses</a></li>
|
||
|
||
</ul>
|
||
|
||
|
||
<li>Specialized BLAST pages
|
||
<ul>
|
||
<li><a href="/SNP/snpblastByChr.html">BLAST against dbSNP</a> (additional
|
||
information about dbSNP is <a href="#dbSNP">above</a>)
|
||
<li><a href="/igblast/">IgBLAST</a> - Analysis of immunoglobulin sequences
|
||
in
|
||
GenBank (described <a href="#IgBLAST">below</a>)
|
||
<li><a href="/VecScreen/VecScreen.html">VecScreen</a> - BLAST-based
|
||
detection of
|
||
vector contamination (described <a href="#VecScreen">below</a>)
|
||
</ul>
|
||
<li>Retrieve results for an existing Request ID (RID)
|
||
<ul>
|
||
<li><a
|
||
href="/blast/Blast.cgi?LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&CMD=Web&PAGE=Forma
|
||
ting
|
||
&NCBI_GI=yes&SHOW_OVERVIEW=on">Retrieve results for an existing Request ID</a>
|
||
for
|
||
up to 24 hours after receiving the RID. (<a
|
||
href="/blast/html/BLASThomehelp.html#EXISTINGRID">more...</a>)
|
||
</ul>
|
||
<li>JavaScript free BLAST pages
|
||
<ul>
|
||
<li><a href="/blast/index.nojs.cgi">Get the BLAST home page with JavaScript
|
||
free
|
||
links</a>
|
||
</ul>
|
||
</ul>
|
||
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ======== Bottom of Border around BLAST home page categories ======== -->
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
<br>
|
||
<!-- ======= END Bottom of Border around BLAST home page categories ======= -->
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/BLAST/blastannounce.html">BLAST Announcements</a> -
|
||
To
|
||
receive announcements about updates and new features, and advance notices about
|
||
upcoming changes in the NCBI BLAST service, see the <a
|
||
href="Summary/email_lists.html">NCBI Announcements Email Lists</a> page.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="BLAST2.x">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/BLAST/qblast.html">BLAST 2.x</a> - A version of BLAST
|
||
(<a
|
||
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_
|
||
uids
|
||
=9254694&dopt=Abstract">Altschul, et al., 1997</a>) that permits gaps in the
|
||
alignments it produces. Assessments of statistical significance are based upon
|
||
prior simulations using random sequences. (<a
|
||
href="/blast/html/BLASThomehelp.html#NTBLAST">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT">QBLAST - A queuing system that allows users to retrieve Gapped
|
||
BLAST results at their convenience and format their results multiple times with
|
||
different formatting options. This system also allows the NCBI to more
|
||
efficiently
|
||
use computational resources, better serving the community. As of Fall 1999, the
|
||
QBLAST system is used for all BLAST searches. (<a
|
||
href="/blast/html/BLASThomehelp.html#NTBLAST">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="MegaBLAST">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO
|
||
_FOR
|
||
MAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=nr&DESCRI
|
||
PTIO
|
||
NS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYP
|
||
E=HT
|
||
ML&HITLIST_SIZE=100&NCBI_GI=on&PAGE=MegaBlast&SERVICE=plain&SET_DEFAULTS.x=34&SE
|
||
T_DE
|
||
FAULTS.y=8&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes">MegaBLAST</a> - permits
|
||
searching
|
||
with batches of ESTs or with large cDNA or genomic sequences. (<a
|
||
href="/blast/html/BLASThomehelp.html#NTBLAST">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="TraceBLAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_SPEC=TraceArchive&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch">BLAST
|
||
against the
|
||
Trace
|
||
Archives</a> - compare nucleotide sequence data against the raw data underlying
|
||
all
|
||
of the sequence generated by various genome projects. Additional information
|
||
about
|
||
the Trace Archive is <a href="#TraceArchive">above</a>.</li></ul></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PHI-BLAST">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=250
|
||
&ALIGNMENT_VIEW=Pairwise&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&
|
||
CDD_
|
||
SEARCH=on&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FORMAT_OBJECT=Alignment
|
||
&FOR
|
||
MAT_TYPE=HTML&HITLIST_SIZE=100&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PA
|
||
GE=P
|
||
roteins&PROGRAM=blastp&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS.x=36&SET_DEFAU
|
||
LTS.
|
||
y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes">PHI-BLAST</a> - Pattern Hit Initiated
|
||
BLAST
|
||
(<a
|
||
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_
|
||
uids
|
||
=9705509&dopt=Abstract">Zhang, et al., 1998</a>) - A program to search a protein
|
||
database using a protein query, seeking only alignments that preserve a
|
||
specified
|
||
pattern contained within the query. (<a
|
||
href="/blast/html/BLASThomehelp.html#AABLAST">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PSI-BLAST">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS
|
||
=250
|
||
&ALIGNMENT_VIEW=Pairwise&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&
|
||
CDD_
|
||
SEARCH=on&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FORMAT_OBJECT=Alignment
|
||
&FOR
|
||
MAT_TYPE=HTML&HITLIST_SIZE=100&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PA
|
||
GE=P
|
||
roteins&PROGRAM=blastp&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS.x=36&SET_DEFAU
|
||
LTS.
|
||
y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes">PSI-BLAST</a> - Position-Specific
|
||
Iterated
|
||
BLAST (<a
|
||
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_
|
||
uids
|
||
=9254694&dopt=Abstract">Altschul, et al., 1997</a>) - A program for searching
|
||
protein databases using protein queries, in order to find other members of the
|
||
same
|
||
protein family. All statistically significant alignments found by BLAST are
|
||
combined into a multiple alignment, from which a position-specific score matrix
|
||
is
|
||
constructed. This matrix is used to search the database for additional
|
||
significant
|
||
alignments, and the process may be iterated until no new alignments are found.
|
||
(<a
|
||
href="/blast/html/BLASThomehelp.html#AABLAST">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="RPS-BLAST">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/cdd/wrpsb.cgi">RPS-BLAST</a> - Reverse
|
||
Position-Specific BLAST - A program used to identify conserved
|
||
domains in a protein query sequence. It does this by comparing a query
|
||
protein sequence to position-specific score matrices that have been prepared
|
||
from conserved domain alignments. The service is accessible through
|
||
<a href="/Structure/cdd/wrpsb.cgi"><b>Conserved Domain Search
|
||
(CD-Search)</b></a>,
|
||
described <a href="#CD-Search">below</a>. A <a
|
||
href="/blast/documents/README.rps">readme</a> file provides additional detail
|
||
about
|
||
the RPS-BLAST program.
|
||
<br>
|
||
<blockquote><i><b>Note:</b></i> RPS-BLAST is a "reverse" version of
|
||
position-specific iterated BLAST (PSI-BLAST), described above. Both RPS-BLAST
|
||
and
|
||
PSI-BLAST use multiple alignments and position-specific score matrices
|
||
(PSSMs) to derive conserved features of a protein family. However,
|
||
RPS-BLAST compares a query sequence against a database of profiles prepared
|
||
from ready-made alignments, while PSI-BLAST builds alignments starting
|
||
from a single protein sequence. The programs also differ in purpose:
|
||
RPS-BLAST is used to identify conserved domains in a query sequence,
|
||
while PSI-BLAST is used to identify other members of the protein family
|
||
to which a query sequence belongs.<blockquote></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="TaxonomyBLAST">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://blast.ncbi.nlm.nih.gov/blast/taxblasthelp.html">Taxonomy BLAST</a> - an
|
||
implementation of Gapped BLAST (2.x) that groups hits by source organism,
|
||
according
|
||
to information in NCBI's Taxonomy database. Species are listed in order of
|
||
sequence
|
||
similarity to the query sequence; the strongest match listed first. Three report
|
||
views are available:
|
||
<ul>
|
||
<li><i>organism report</i> - sorts the BLAST hits according to species, so that
|
||
all
|
||
of the hits to the same organism will appear together
|
||
<li><i>lineage report</i> - gives a simplified view of the relationships between
|
||
the
|
||
organisms, according to their classification in the taxonomy database. This
|
||
report
|
||
is "focused" on the organism which yielded the strongest BLAST hit. It answers
|
||
the
|
||
question, "how closely are the organisms in the BLAST hit list related to the
|
||
query
|
||
sequence according to the taxonomy database?"
|
||
<li><i>taxonomy report</i> - provides a more detailed report about the
|
||
relationships among all of the organisms found in the BLAST hit list, including
|
||
a
|
||
summary of the taxa that are represented, the number of species and subspecies,
|
||
and
|
||
the number of BLAST hits at each node in the taxonomic hierarchy.
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PrimerBLAST"></a>
|
||
<table border="0" cellspacin="5" width="90%" bgcolor="FFFFFF">
|
||
<tr>
|
||
<td class="text"><a href="/tools/primer-blast/index.cgi?LINK_LOC=BlastHome">Primer-BLAST</a> - find primers
|
||
specific to a PCR template.</td>
|
||
|
||
<a NAME="BLAST2Sequences"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&LINK_LOC=align2seq">BLAST
|
||
2 Sequences</a> - A BLAST-based
|
||
tool
|
||
for aligning two nucleotide or protein sequences, producing a pairwise DNA-DNA
|
||
or
|
||
protein-protein sequence comparison. (<a
|
||
href="/blast/html/BLASThomehelp.html#BLAST2SEQ">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="IgBLAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/igblast/">IgBLAST</a> - IgBLAST was developed to
|
||
facilitate analysis of immunoglobulin sequences in GenBank. It allows
|
||
blastp or blastn searches of either the nr database or a special database
|
||
of Immunoglobulin (Ig) germline V (variable region) genes. Searches may
|
||
be limited to either human or mouse genes. IgBLAST performs three main
|
||
functions: (1) reports the variable, D, or J regions that most closely
|
||
match the query sequence; (2) annotates the immunoglobulin domains
|
||
(FWR1 through FWR3) according to Kabat et al.; and (3) for searches
|
||
against the nucleotide nr or protein nr database, simplifies the
|
||
process of identifying related sequences by matching the IgBLAST hits
|
||
to the closest germline V genes. (<a
|
||
href="/blast/html/BLASThomehelp.html#SPECBLAST">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="BLink"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/static/blinkhelp.html">BLink</a> - BLink
|
||
("BLAST
|
||
Link") displays the results of BLAST searches that have been done for every
|
||
protein
|
||
sequence in the Entrez Proteins data domain. <b>To access it</b>, follow the
|
||
Blink
|
||
link displayed beside any hit in the results of an Entrez Proteins search. In
|
||
contrast to Entrez's "Related Sequences" feature, which lists the titles of
|
||
similar
|
||
sequences, BLink displays the graphical output of pre-computed blastp results
|
||
against the protein non-redundant (nr) database. The output includes the
|
||
positions
|
||
of up to 200 BLAST hits on the query sequence, scores, and alignments. (View <a
|
||
href="http://www.ncbi.nlm.nih.gov/sutils/blink.cgi?pid=4557757">sample BLink
|
||
output
|
||
for human MLH1 protein</a>.) BLink offers a variety of display options,
|
||
including
|
||
the distribution of hits by taxonomic grouping, the best hit to each organism,
|
||
the
|
||
protein domains in the query sequence, similar sequences that have known 3-D
|
||
structures, and more.
|
||
Additional options allow you to specify which taxa you would like to exclude,
|
||
increase or decrease the BLAST cutoff score, or filter the BLAST hits to show
|
||
only
|
||
those from a specific source database, such as RefSeq or Swiss-Prot. See
|
||
the
|
||
<a href="/sutils/static/blinkhelp.html">BLink help document</a> for additional
|
||
information.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="BLASTEmailServer"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Genbank/GenBankEmail.html">BLAST E-mail server</a> -
|
||
an
|
||
e-mail-based sequence similarity search service; this was <b>discontinued on
|
||
June
|
||
17, 2002</b> because of limited usage. Most BLAST searchers are now done
|
||
through <a
|
||
href="/BLAST/">BLAST web page.</a></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/blast/blastcl3/">Network
|
||
BLAST</a>
|
||
- a TCP/IP-based client-server version of WWW Entrez. Makes a direct connection
|
||
with
|
||
the NCBI databases over the Internet to retrieve data. No web browser is
|
||
required.
|
||
Client software is available for PC, Mac, and Unix on the FTP site at
|
||
ftp://ftp.ncbi.nih.gov/blast/blastcl3/</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/blast/executables/">Stand-alone
|
||
BLAST</a> - download BLAST executables for local use from
|
||
ftp://ftp.ncbi.nih.gov/blast/executables/. Binaries are provided for IRIX 6.2,
|
||
Solaris 2.6, DEC OSF1 (ver. 4.0d), LINUX, and Win32 systems. Please read the <a
|
||
href="/blast/executables/README.bls">README file</a> in the ftp directory for
|
||
more
|
||
information. <a href="ftp://ftp.ncbi.nih.gov/blast/db/">BLAST databases</a> also
|
||
available for downloading. There is also some information on setting up
|
||
Standalone
|
||
BLAST at the NHGRI site at <a
|
||
href="http://genome.nhgri.nih.gov/blastall/blast_install/">http://genome.nhgri.n
|
||
ih.g
|
||
ov/blastall/blast_install</a>.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN TOOLS: NUCLEOTIDE SEQUENCE ANALYSIS======== -->
|
||
<a NAME="NucleotideSequenceAnalysis"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Nucleotide Sequence Analysis</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/BLAST/">BLAST</a> - see sequence similarity
|
||
searching, <a
|
||
href="#BLAST">above</a>, for a complete list of BLAST programs.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ePCR"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/e-pcr/">e-PCR - Electronic PCR</a> - compare a
|
||
query sequence to a database of mapped sequence-tagged sites (STSs) to find a
|
||
possible map location for the query sequence, or compare a query STS to a database
|
||
of nucleotide sequences to identify the sequences that contain the STS.
|
||
<!-- E-PCR finds STSs in DNA sequences by searching
|
||
for
|
||
subsequences that closely match the PCR primers present in mapped markers. The
|
||
subsequences must have the correct order, orientation, and spacing that they
|
||
could
|
||
plausibly prime the amplification of a PCR product of the correct molecular
|
||
weight.
|
||
e-PCR searches against data in NCBI's <b>UniSTS</b>, <a
|
||
href="#UniSTS">described</a> in the Molecular Databases/Nucleotide Sequences
|
||
section of this guide. (The <a href="/STS/">original version</a> of
|
||
e-PCR
|
||
searches only against dbSTS.) --> e-PCR can be used on the WWW, or the
|
||
software can be downloaded from the <a
|
||
href="ftp://ftp.ncbi.nih.gov/pub/schuler/e-PCR/">/pub/schuler/e-PCR
|
||
directory</a> of the NCBI ftp site. Additional information is provided by <a
|
||
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Ab
|
||
stract&list_uids=9149949">Schuler, G.D.</a> There are two versions of e-PCR:
|
||
|
||
<ul>
|
||
|
||
<li><a href="http://www.ncbi.nlm.nih.gov/sutils/e-pcr/forward.cgi">Forward
|
||
e-PCR</a> - Search STS database with a query sequence. Electronic PCR (e-PCR) is
|
||
computational procedure that is used to identify sequence tagged sites(STSs),
|
||
within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching
|
||
for subsequences that closely match the PCR primers and have the correct order,
|
||
orientation, and spacing that could represent the PCR primers used to generate
|
||
known STSs.</li>
|
||
|
||
<li><a href="http://www.ncbi.nlm.nih.gov/sutils/e-pcr/reverse.cgi">Reverse
|
||
e-PCR</a> - Search sequence database with STS. The main motivation for
|
||
implementing reverse searching (called Reverse e-PCR) was to make it feasible to
|
||
search the human genome sequence and other large genomes. The new version of e-PCR
|
||
provides a search mode using a query sequence against a sequence database.</li>
|
||
|
||
</ul>
|
||
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<a NAME="EntrezGeneNucSeqAnalysis"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=gene">Entrez Gene</a> - as <a
|
||
href="#EntrezGene">described</a> in the Molecular Databases/Genes section of this
|
||
guide, each Entrez Gene record encapsulates a wide range of information for a
|
||
given gene and organism. When possible, the information includes results of
|
||
analyses that have been done on the sequence data. The amount and type of
|
||
information presented depend on what is available for a particular gene and
|
||
organism and can include:
|
||
(1) graphic summary of the genomic context, intron/exon structure, and
|
||
flanking genes,
|
||
(2) link to a graphic view of the mRNA sequence, which in turn shows
|
||
biological features such as CDS, SNPs, etc.,
|
||
(3) links to gene ontology and phenotypic information,
|
||
(4) links to corresponding protein sequence data and conserved domains,
|
||
(5) links to related resources, such as mutation databases.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/projects/Malaria/">Malaria Genetics and Genomics</a>
|
||
-
|
||
provides data and information relevant to malaria genetics and genomics.
|
||
Resources
|
||
include organism specific sequence BLAST databases (<i>Plasmodium falciparum</i>
|
||
only, all <i>Plasmodium</i>, and all <i>Toxoplasma</i>). More about the Malaria
|
||
genome resources <a href="#MalariaGenome">below</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ModelMaker"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/static/ModelMakerHelp.html">Model Maker</a> -
|
||
allows you to view the evidence (mRNAs, ESTs, and gene predictions) that was
|
||
aligned
|
||
to assembled genomic sequence in order to build a gene model, and to edit the
|
||
model
|
||
by selecting or removing putative exons. You can then view the mRNA sequence
|
||
and
|
||
potential ORFs for the edited model, and save the mRNA sequence data for use in
|
||
other programs. Model Maker is accessible from sequence maps that were analyzed
|
||
at
|
||
NCBI and displayed in <b>Map Viewer</b> (described <a
|
||
href="#MapViewer">above</a>).
|
||
To see an <b>example</b>, follow the <b>"mm" link</b> beside any gene
|
||
annotated on the <a
|
||
href="http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?org=hum&chr=1&maps=ideogr,loc
|
||
&ver
|
||
bose=on">human "Gene_Sequence" map</a> in the Map Viewer. (More info about
|
||
human
|
||
data in Map Viewer is given <a href="#MapViewerHuman">above</a>.)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ORFFinder"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/gorf/gorf.html">ORF Finder</a> - graphical analysis
|
||
tool
|
||
which finds all open reading frames of a selected minimum size in a user's
|
||
sequence
|
||
or in a sequence already in the database. Designed for prokaryotic sequences.
|
||
Identifies all open reading frames using the standard or alternative genetic
|
||
codes.
|
||
The deduced amino acid sequence can be saved in various formats and searched
|
||
against
|
||
the sequence database using the WWW BLAST server. The ORF Finder is also
|
||
packaged
|
||
with the <a href="/Sequin/">Sequin</a> sequence submission software. The <a
|
||
href="ftp://ftp.ncbi.nih.gov/pub/tatiana/orf/">stand alone program</a> can be
|
||
downloaded from NCBI ftp site.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ProtEST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/ProtEST/">ProtEST</a> - a tool that presents
|
||
a graphical view of matches between nucleotide sequences in UniGene and possible
|
||
translational products. To generate the alignments, the 6-frame translations
|
||
of mRNA and EST sequences in UniGene are compared to protein sequences using BLASTX
|
||
with -e 1e-6. The translated nucleotide sequences are compared with proteins
|
||
from a number of model organisms and the best match in each organism is recorded.
|
||
ProtEST links are displayed in UniGene (<a href="#UniGene">description</a>)
|
||
reports in the section on model organism protein similarities.
|
||
<!-- [Text from 03/2003 version of "Genomic Biology Resources" fact sheet:
|
||
Pre-computed BLAST alignments between protein sequences from eight model organisms,
|
||
including H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elgans, S. cerevisiae,
|
||
A. thaliana, and E. coli, and the six-frame translations of UniGene nucleotide sequences.
|
||
ProtEST links are displayed in UniGene reports in the section on model organism protein
|
||
similarities.] --></td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/pasc/viridty.cgi?textpage=overview">PASC (PAirwise Sequence Comparison)</a> - a web tool for analysis of pairwise identity distribution within <b>viral families</b>. The identities are pre-computed for every pair within the families and with distribution plotted in a form of histogram where each bar corresponds to an interval of identities. Only complete genomes should be used as query sequences. The results from partial sequences are not suitable for the purpose of this tool. After you submit your sequence, PASC will start computing pairwise identities between the external genome and the existing genome sequences of the family. At the end of the process, you will be presented with the list of 15 closest matches to the genome within the family. The <a href="/sutils/pasc/viridty.cgi?textpage=documentation">documentation</a> provides more details about using PASC.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/retroviruses/">Retroviruses Resources</a> - A
|
||
collection
|
||
of resources specifically designed to support the research of retroviruses.
|
||
Resources include a genotyping tool that uses the BLAST algorithm to identify
|
||
the
|
||
genotype of a query sequence; an alignment tool for global alignment of multiple
|
||
sequences; an HIV-1 automatic sequence annotation tool; and annotated maps of 16
|
||
retroviruses viewable in GenBank, FASTA, and graphic formats, with links to
|
||
associated sequence records.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SAGEmap"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/SAGE/">SAGEmap</a> - SAGEmap provides a tool for
|
||
performing statistical tests designed specifically for differential-type
|
||
analyses of
|
||
SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries
|
||
generated by individual labs as well as those generated by the Cancer Genome
|
||
Anatomy
|
||
Project (CGAP, described <a href="#CGAP">above</a>), which have been submitted
|
||
to
|
||
Gene Expression Omnibus (GEO, described <a href="#GEO">above</a>). Gene
|
||
expression
|
||
profiles that compare the expression in different SAGE libraries are also
|
||
available
|
||
on the Entrez GEO Profiles pages. It is possible to enter a query sequence in
|
||
the
|
||
SAGEmap resource to determine what SAGE tags are in the sequence, then map to
|
||
associated SAGEtag records and view the expression of those tags in different
|
||
CGAP
|
||
SAGE libraries.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Sequin/index.html">Sequin</a> - A submission tool
|
||
that
|
||
includes <a href="#ORFFinder">ORF Finder</a>, an alignment viewer/editor, and a
|
||
link
|
||
to <a href="#Entrez">Entrez</a>. More information about Sequin is <a
|
||
href="#Sequin">above</a>.</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<a NAME="Spidey"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/IEB/Research/Ostell/Spidey/">Spidey</a> -
|
||
mRNA-to-genomic
|
||
alignment program that was designed to find good alignments regardless of intron
|
||
size, and to avoid getting confused by nearby pseudogenes and paralogs. It uses
|
||
a
|
||
combination of alignment algorithms and heuristics to construct its models.
|
||
Spidey
|
||
has been optimized for both intraspecies and interspecies alignments. (See <a href="/IEB/Research/Ostell/Spidey/spideydoc.html">Spidey documentation</a> for more information.)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Splign"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/splign/">Splign</a> -
|
||
a utility for computing cDNA-to-Genomic, or spliced sequence alignments.
|
||
It is based on a variation of the Needleman<61>Wunsch global alignment algorithm and
|
||
specifically accounts for introns and splice signals. It is due to this algorithm that
|
||
Splign is accurate in determining splice sites and tolerant to sequencing errors.
|
||
Splign also uses BLAST hits to identify possible locations of genes and their
|
||
duplications on genomic sequences and to speed up the core dynamic programming.
|
||
(See <a href="/sutils/splign/splign.cgi?textpage=documentation">Splign documentation</a> for more information.)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="UniGeneDDD"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/info_ddd.shtml">UniGene DDD</a> - Digital
|
||
Differential Display - an online tool to compare computed gene expression
|
||
profiles
|
||
between selected cDNA libraries. Using a statistical test, genes whose
|
||
expression
|
||
levels differ significantly from one tissue to the next are identified and shown
|
||
to
|
||
the user. <a href="#UniGene">Additional information</a> about UniGene is in the
|
||
<a
|
||
href="#Genes">Molecular Databases/Genes</a> section.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="VecScreen"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/VecScreen/VecScreen.html">VecScreen</a> - a tool for
|
||
identifying segments of a nucleic acid sequence that may be of vector, linker or
|
||
adapter origin prior to sequence analysis or submission. VecScreen was
|
||
developed to
|
||
combat the problem of vector contamination in public sequence databases. It is
|
||
also
|
||
useful to run a new sequence through VecScreen before performing any kind of
|
||
analysis on the sequence, since the presence of vector sequences can lead to
|
||
misleading BLAST hits, etc. VecScreen compares a query sequence against the
|
||
<b>UniVec</b> database, described <a href="#UniVec">above</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN TOOLS: PROTEIN SEQUENCE ANALYSIS======== -->
|
||
<a NAME="ProteinSequenceAnalysis"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Protein Sequence Analysis and
|
||
Proteomics</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/BLAST/">BLAST</a> - see sequence similarity
|
||
searching, <a
|
||
href="#BLAST">above</a>, for a complete list of BLAST programs.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/static/blinkhelp.html">BLink</a> - BLink
|
||
("BLAST
|
||
Link") displays the results of BLAST searches that have been done for every
|
||
protein
|
||
sequence in the Entrez Proteins data domain. <b>To access it</b>, follow the
|
||
BLink
|
||
link displayed beside any hit in the results of an Entrez Proteins search. In
|
||
contrast to Entrez's "Related Sequences" feature, which lists the titles of
|
||
similar
|
||
sequences, BLink displays the graphical output of pre-computed blastp results
|
||
against the protein non-redundant (nr) database. The output includes the
|
||
positions
|
||
of up to 200 BLAST hits on the query sequence, scores, and alignments. (View <a
|
||
href="http://www.ncbi.nlm.nih.gov/sutils/blink.cgi?pid=4557757">sample BLink
|
||
output
|
||
for human MLH1 protein</a>.) BLink offers a variety of display options,
|
||
including
|
||
the distribution of hits by taxonomic grouping, the best hit to each organism,
|
||
the
|
||
protein domains in the query sequence, similar sequences that have known 3-D
|
||
structures, and more.
|
||
Additional options allow you to specify which taxa you would like to exclude,
|
||
increase or decrease the BLAST cutoff score, or filter the BLAST hits to show
|
||
only
|
||
those from a specific source database, such as RefSeq or Swiss-Prot. See
|
||
the
|
||
<a href="/sutils/static/blinkhelp.html">BLink help document</a> for additional
|
||
information.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CD-Search"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/cdd/cdd.shtml">CD-Search</a> -
|
||
The Conserved Domain Search Service (CD-Search) can be used to identify
|
||
the conserved domains present in a protein sequence. CD-Search
|
||
uses RPS-BLAST (described <a href="#RPS-BLAST">above</a>) to compare
|
||
a query sequence against position-specific score matrices that
|
||
have been prepared from conserved domain alignments present in
|
||
the Conserved Domain Database (CDD) (described <a href="#CDD">above</a>).
|
||
Hits can be displayed as a pairwise alignment of the query sequence
|
||
with a representative domain sequence, or as a multiple alignment.
|
||
Alignments are also mapped to known 3-dimensional structures,
|
||
and can be displayed using Cn3D (described <a href="#Cn3D">above</a>).
|
||
In the Cn3D display, residues in sequence alignments are variously colored,
|
||
based on their degree of conservation. (<a
|
||
href="/blast/html/BLASThomehelp.html#CDSEARCH">more...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Cognitor"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/COG/old/xognitor.html">COGnitor</a> - compare your
|
||
sequence to the COGs database (described <a href="#COGs">above</a>) to identify
|
||
the
|
||
cluster of orthologous groups to which it belongs. A stand-alone <a
|
||
href="ftp://ftp.ncbi.nih.gov/pub/tatusov/dignitor/">dignitor</a> program is also
|
||
available. It runs cognitor in batch mode, comparing a large group of proteins
|
||
to
|
||
the COGs database, and can be downloaded from the ftp site.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="CDART"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/lexington/lexington.cgi?cmd=rps">Conserved
|
||
Domain Architecture Retrieval Tool (CDART)</a> - When given a protein query
|
||
sequence, CDART displays the functional domains that make up the protein and
|
||
lists
|
||
proteins with similar domain architectures. The functional domains for a
|
||
sequence
|
||
are found by comparing the protein sequence to a database of conserved domain
|
||
alignments, CDD (described <a href="#CDD">above</a>), using RPS-BLAST (described
|
||
<a
|
||
href="#RPS-BLAST">below</a>).
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="OMSSA"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://pubchem.ncbi.nlm.nih.gov/omssa">Open Mass
|
||
Spectrometry Search Algorithm (OMSSA)</a> - a public search service that allows
|
||
proteomics researchers to submit the mass spectra of peptides and proteins for
|
||
identification. OMSSA then compares these mass spectra to theoretical ions
|
||
generated from databases of known protein sequences and then ranks the results
|
||
using a score derived from classical hypothesis testing. References available
|
||
from the OMSSA home page describe the OMSSA algorithm and its validation.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/ProtEST/">ProtEST</a> - a tool that presents
|
||
a graphical view of matches between nucleotide sequences in UniGene and possible
|
||
translational products. To generate the alignments, the 6-frame translations
|
||
of mRNA and EST sequences in UniGene are compared to protein sequences using BLASTX
|
||
with -e 1e-6. The translated nucleotide sequences are compared with proteins
|
||
from a number of model organisms and the best match in each organism is recorded.
|
||
ProtEST links are displayed in UniGene (<a href="#UniGene">description</a>)
|
||
reports in the section on model organism protein similarities.
|
||
<!-- [Text from 03/2003 version of "Genomic Biology Resources" fact sheet:
|
||
Pre-computed BLAST alignments between protein sequences from eight model organisms,
|
||
including H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elgans, S. cerevisiae,
|
||
A. thaliana, and E. coli, and the six-frame translations of UniGene nucleotide sequences.
|
||
ProtEST links are displayed in UniGene reports in the section on model organism protein
|
||
similarities.] --></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="TaxPlot">
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/taxik2.cgi">TaxPlot</a> - a tool for 3-way
|
||
comparisons of genomes on the basis of the protein sequences they encode. To use
|
||
TaxPlot, one selects a reference genome to which two other genomes are compared.
|
||
Pre-computed BLAST results are then used to plot a point for each predicted
|
||
protein
|
||
in the reference genome, based on the best alignment with proteins in each of
|
||
the
|
||
two genomes being compared.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<br>
|
||
|
||
<!-- CATEGORY WITHIN TOOLS: 3-D STRUCTURE DISPLAY AND SIMILARITY SEARCHING -->
|
||
|
||
<a NAME="StructureTools"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">3-D Structure Display and
|
||
Similarity
|
||
Searching</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<a NAME="Cn3D"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/CN3D/cn3d.shtml">Cn3D</a> - "See in 3-D," a
|
||
structure and sequence alignment viewer for NCBI databases. It allows viewing
|
||
of
|
||
3-D structures and sequence-structure or structure-structure alignments. Cn3D
|
||
can
|
||
work as a helper application to your browser, or as a client-server application
|
||
that
|
||
retrieves structure records from MMDB (described <a href="#MMDB">above</a>)
|
||
directly
|
||
over the internet. The <a href="/Structure/CN3D/cn3d.shtml">Cn3D home page</a>
|
||
provides access to information on how to <a
|
||
href="/Structure/CN3D/cn3dinstall.shtml">install</a> the program, a <a
|
||
href="/Structure/CN3D/cn3dtut.shtml">tutorial</a> to get started, and a
|
||
comprehensive <a href="/Structure/CN3D/cn3dhelp.shtml">help document</a>.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="VAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/VAST/vast.html">VAST</a> - Vector Alignment
|
||
Search Tool - a computer algorithm developed at NCBI and used to identify
|
||
similar
|
||
protein 3-dimensional structures. The "structure neighbors" for every structure
|
||
in
|
||
MMDB are pre-computed and accessible via links on the MMDB Structure Summary
|
||
pages.
|
||
These neighbors can be used to identify distant homologs that cannot be
|
||
recognized
|
||
by sequence comparison alone.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="VASTSearch"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Entrez/">VAST search</a> - - structure-structure
|
||
similarity search service. Compares 3D coordinates of a newly determined
|
||
protein
|
||
structure to those in the MMDB/PDB database. VAST Search computes a list of
|
||
structure neighbors that you may browse interactively, viewing superpositions
|
||
and
|
||
alignments by molecular graphics.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/cdd/wrpsb.cgi">CD-Search</a> -
|
||
The Conserved Domain Search Service (CD-Search) can be used to identify
|
||
the conserved domains present in a protein sequence. CD-Search
|
||
uses RPS-BLAST (described <a href="#RPS-BLAST">above</a>) to compare
|
||
a query sequence against position-specific score matrices that
|
||
have been prepared from conserved domain alignments present in
|
||
the Conserved Domain Database (CDD) (described <a href="#CDD">above</a>).
|
||
Hits can be displayed as a pairwise alignment of the query sequence
|
||
with a representative domain sequence, or as a multiple alignment.
|
||
Alignments are also mapped to known 3-dimensional structures,
|
||
and can be displayed using Cn3D (described <a href="#Cn3D">above</a>).
|
||
In the Cn3D display, residues in sequence alignments are variously colored,
|
||
based on their degree of conservation.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="Threading"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/RESEARCH/threading.shtml">Threading</a> -
|
||
As
|
||
part of NCBI's Computational Biology Branch (described <a
|
||
href="#CBB">above</a>),
|
||
the Structure group, led by Dr. Steve Bryant, conducts research in protein
|
||
threading. Protein threading predicts the three-dimensional structure of a
|
||
protein
|
||
sequence by threading it through known structures and calculating its energy.
|
||
The
|
||
experimental software developed by the NCBI Structure group is available on the
|
||
<a
|
||
href="ftp://ftp.ncbi.nih.gov/pub/pkb/">FTP</a> site. A <a
|
||
href="ftp://ftp.ncbi.nih.gov/pub/pkb/README">readme</a> file provides more
|
||
information as well as references.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<br>
|
||
|
||
<!-- ========CATEGORY WITHIN TOOLS: GENOME ANALYSIS======== -->
|
||
<a NAME="GenomeAnalysisTools"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Genome Analysis Tools</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=Genome">Entrez Genome</a> -
|
||
whole
|
||
genomes of over 1000 organisms. The genomes represent both completely sequenced
|
||
organisms and those for which sequencing is in progress. All three main domains
|
||
of
|
||
life - <a
|
||
HREF="/genomes/static/eub_g.html">bacteria</a>,
|
||
<a
|
||
HREF="/genomes/static/a_g.html">archaea,</a>
|
||
and <a
|
||
HREF="/genomes/static/euk_g.html">eukaryota</a>
|
||
- are represented, as well as many <a
|
||
HREF="/genomes/VIRUSES/viruses.html">viruses</a>,
|
||
<a
|
||
HREF="/genomes/static/phg.html">phages</a>,
|
||
<a
|
||
HREF="/genomes/static/vid.html">viroids</a>,
|
||
<a
|
||
HREF="/genomes/static/o.html">plasmids</a>,
|
||
and <a
|
||
HREF="/genomes/ORGANELLES/organelles.html">organelles.</a>. Entrez Genome
|
||
provides
|
||
graphical overviews of complete genomes/chromosomes, and the ability to explore
|
||
regions of interest in progressively greater detail. <a
|
||
href="#ProtTaxTable">ProtTables and TaxTables</a> are provided for organisms on
|
||
which analyses have been done by NCBI staff.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/mapview/">Map Viewer</a> - shows integrated views of
|
||
chromosome maps for many organisms. Used to view the NCBI assembly of complete
|
||
genomes, including human, Map Viewer is a valuable tool for the identification
|
||
and
|
||
localization of genes, particularly those that contribute to diseases. <a
|
||
href="#MapViewer">Additional information</a> about Map Viewer is provided in the
|
||
<a
|
||
href="#Genomes">Genomes and Maps</a> section of this guide.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sky/">SKY/M-FISH & CGH Database</a> - The NCI and
|
||
NCBI
|
||
SKY/M-FISH and CGH Database is a repository of publicly submitted data from
|
||
Spectral
|
||
Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and
|
||
Comparative Genomic Hybridization (CGH),
|
||
which are complementary fluorescent molecular cytogenetic techniques.
|
||
SKY/M-FISH permits the simultaneous visualization of each human
|
||
or mouse chromosome in a different color, facilitating the identification of
|
||
chromosomal aberrations; CGH can
|
||
be used to generate a map of DNA copy number changes in tumor genomes.
|
||
Collaborative
|
||
project with the National Cancer Institute. (<a
|
||
href="/sky/show_html_frag.cgi?filename=protocol.html_frag&header=Instructions+fo
|
||
r+SKY+or+M-FISH+and+CGH+data+submission&title=Instructions+for+SKY+or+M-FISH+and
|
||
+CGH+data+submission">data
|
||
submission instructions...</a>)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/sutils/pasc/viridty.cgi?textpage=overview">PASC (PAirwise Sequence Comparison)</a> - a web tool for analysis of pairwise identity distribution within <b>viral families</b>. The identities are pre-computed for every pair within the families and with distribution plotted in a form of histogram where each bar corresponds to an interval of identities. Only complete genomes should be used as query sequences. The results from partial sequences are not suitable for the purpose of this tool. After you submit your sequence, PASC will start computing pairwise identities between the external genome and the existing genome sequences of the family. At the end of the process, you will be presented with the list of 15 closest matches to the genome within the family. The <a href="/sutils/pasc/viridty.cgi?textpage=documentation">documentation</a> provides more details about using PASC.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/retroviruses/">Retrovirus Resources</a> - A
|
||
collection of resources specifically designed to support the research of retroviruses.
|
||
Resources include a genotyping tool that uses the BLAST algorithm to identify the genotype
|
||
of a query sequence; an alignment tool for global alignment of multiple sequences;
|
||
an HIV-1 automatic sequence annotation tool; and annotated maps of 16 retroviruses
|
||
viewable in GenBank, FASTA, and graphic formats, with links to associated sequence
|
||
records.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN TOOLS: GENE EXPRESSION======== -->
|
||
<a NAME="GeneExpressionTools"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Gene Expression Tools</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/geo/">Gene Expression Omnibus (GEO)</a> - provides
|
||
several tools to assist with the visualization and exploration of GEO data.
|
||
Datasets may be viewed as hierarchical cluster heat maps, providing insight into
|
||
the
|
||
relationships between samples and co-regulated genes. Individual gene
|
||
expression
|
||
profiles showing significant differences between experimental subsets may be
|
||
located
|
||
using average subset rank value comparisons. Related gene expression profiles
|
||
may
|
||
be identified on the basis of sequence similarity, profile similarity, or
|
||
homology.
|
||
Indicators of dataset normalization quality are provided as distribution graphs,
|
||
and
|
||
by flagging outliers. Links to other
|
||
NCBI sequence, mapping and publication database resources are provided where
|
||
possible. (<a href="#GEO">More information</a> about GEO is provided in the
|
||
Molecular Databases/Gene Expression section of this file.)<br></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/SAGE/">SAGEmap</a> - SAGEmap provides a tool for
|
||
performing statistical tests designed specifically for differential-type
|
||
analyses of
|
||
SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries
|
||
generated by individual labs as well as those generated by the Cancer Genome
|
||
Anatomy
|
||
Project (CGAP, described <a href="#CGAP">above</a>), which have been submitted
|
||
to
|
||
Gene Expression Omnibus (GEO, described <a href="#GEO">above</a>). Gene
|
||
expression
|
||
profiles that compare the expression in different SAGE libraries are available
|
||
on
|
||
the <a href="/entrez/query.fcgi?db=geo">Entrez GEO Profiles</a> pages. It is
|
||
also
|
||
possible to enter a query sequence in the <a href="/SAGE/">SAGEmap</a> resource
|
||
to
|
||
determine what SAGE tags are in the sequence, then map to associated SAGEtag
|
||
records
|
||
and view the expression of those tags in different CGAP SAGE libraries. (<a
|
||
href="#SAGEmap">More information</a> about SAGEmap is provided in the Molecular
|
||
Databases/Gene Expression section of this file.)
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/CGAP/">Cancer Genome Anatomy Project (CGAP)</a> - an
|
||
interdisciplinary program to identify the human genes expressed in different
|
||
cancerous states, based on cDNA (EST) libraries, and to determine the molecular
|
||
profiles of normal, precancerous, and malignant cells. CGAP is a collaboration
|
||
among the National Cancer Institute, the NCBI, and numerous research labs.
|
||
(Related
|
||
resources are listed under <a href="#CancerResearch">human genome/cancer
|
||
research</a>.) The following tools are provided by the National Cancer
|
||
Institute
|
||
(NCI) through their CGAP web page:
|
||
<ul>
|
||
<li><a href="http://cgap.nci.nih.gov/Tissues/LibrarySummarizer">Gene Library
|
||
Summarizer (GLS)</a> - Tool that finds all the genes in a specific cDNA library
|
||
or
|
||
group of libraries. <!-- Tool that searches for cDNA libraries by gene and
|
||
returns
|
||
library name and expression level. --></li>
|
||
<li><a href="http://cgap.nci.nih.gov/Tissues/xProfiler">cDNA Expression Profiler
|
||
(xProfiler)</a> - an online tool to compare computed gene expression profiles
|
||
between selected cDNA libraries. </li>
|
||
<li><a href="http://cgap.nci.nih.gov/Tissues/GXS">Differential Gene Expression
|
||
Displayer (DGED) </a> - distinguishes statistical differences in gene expression
|
||
between two pools of libraries. </li>
|
||
<!-- li><a href="/SAGE/">NCBI's Serial Analysis of Gene Expression Map </a> - An
|
||
online tool to compare computed gene expression profiles between selected SAGE
|
||
(Serial Analysis of Gene Expression) libraries. Also includes a comprehensive
|
||
analysis of SAGE tags in human GenBank records, in which a UniGene identifier is
|
||
assigned to each human sequence that contains a SAGE tag. (See additional
|
||
information about SAGEmap, <a href="#SAGEmap">below</a>.)</li -->
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/UniGene/info_ddd.shtml">UniGene DDD</a> - Digital
|
||
Differential Display - an online tool to compare computed gene expression
|
||
profiles
|
||
between selected cDNA libraries. Using a statistical test, genes whose
|
||
expression
|
||
levels differ significantly from one tissue to the next are identified and shown
|
||
to
|
||
the user. <a href="#UniGene">Additional information</a> about UniGene is in the
|
||
<a
|
||
href="#Genes">Molecular Databases/Genes</a> section.</td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- =============================END_TOOLS=========================== -->
|
||
|
||
<!-- ========================= RESEARCH ========================= -->
|
||
<a NAME="Research"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" class="H3a">Research at NCBI</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" class="H4a"><a
|
||
href="/CBBresearch/">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<a NAME="CBB"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/CBBresearch/">Computational Biology Branch Home
|
||
Page</a>
|
||
- Overview of the research program in the Computational Biology Branch (CBB) of
|
||
NCBI
|
||
and a list of Senior Investigators. The research programs focus on theoretical,
|
||
analytical, and applied approaches to a broad range of fundamental problems in
|
||
molecular biology, including biomolecular structures, genome analysis, theory of
|
||
sequence analysis, hardware design, software and database design, and text
|
||
retrieval
|
||
and document analysis.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ResearchProjects"></a>
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://www.ncbi.nlm.nih.gov/Web/Research/proj.html">Research Projects</a>
|
||
-
|
||
List of research projects pertaining to biomolecular structures, genome
|
||
analysis,
|
||
theory of sequence analysis, hardware design, software and database design, and
|
||
text
|
||
retrieval and document analysis. Links are also provided to a staff
|
||
bibliography
|
||
and the full text of selected publications.</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<a NAME="SeniorInvestigatorsInPubMed"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/CBBresearch/senior.html">Senior Investigators in
|
||
PubMed</a> - publications written by senior investigators in the NCBI
|
||
Computational
|
||
Biology Branch and represented in the <a href="#PubMed">PubMed</a> database.
|
||
The
|
||
PubMed records include links to publisher web sites and/or full text articles
|
||
when
|
||
available.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SeminarSchedule"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/CBBresearch/Seminar/">Seminar Schedule</a> - Seminars
|
||
held at NCBI on a wide range of molecular biology and mathematical topics.
|
||
These
|
||
seminars are open to the NIH community and the general public, and are presented
|
||
by
|
||
NCBI staff as well as visiting scientists.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="PostdoctoralFellows"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="Summary/postdoc.html">Postdoctoral Fellowships</a> -
|
||
general information, application procedure</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="StaffBibliography"></a>
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://www.ncbi.nlm.nih.gov/Web/Research/Bib/index.html">Staff
|
||
Bibliography</a> - A list of published and in-press papers and monographic
|
||
chapters
|
||
written by current and former NCBI staff. Includes links to corresponding
|
||
PubMed
|
||
records. Selected papers can also be seen on the full-text page, below.</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<a NAME="StaffFullText"></a>
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://www.ncbi.nlm.nih.gov/Web/Research/Papers/index.html">Full Text of
|
||
Selected Staff Publications</a> - full text of selected published and in-press
|
||
papers and monographic chapters written by current and former NCBI staff.</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<br>
|
||
|
||
<!-- ====================== END RESEARCH ========================= -->
|
||
|
||
<!-- ==================== SOFTWARE ENGINEERING ====================== -->
|
||
<a NAME="SoftwareEngineering"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" CLASS="H3a">SoftwareEngineering</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a href="/IEB/">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<a NAME="IEB"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/IEB/">Information Engineering Branch Home Page</a> -
|
||
Overview of the functions of the Information Engineering Branch (IEB) of NCBI,
|
||
which
|
||
is responsible for designing and building NCBI's production software and
|
||
databases.
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="ToolBox"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/IEB/ToolBox/">NCBI ToolBox</a> - Supported software
|
||
tools
|
||
from IEB. Describes the three components of the ToolBox: data model, data
|
||
encoding,
|
||
and programming libraries. Provides access to documentation for the data model,
|
||
C
|
||
toolkit, C++ toolkit, NCBI Toolkit Source Browser, XML demo program, XML DTDs,
|
||
and
|
||
the <a href="ftp://ftp.ncbi.nih.gov/toolbox/">FTP site</a>. Additional
|
||
information
|
||
about the FTP site is provided <a href="#FTP_ToolBox">below</a>.</tr>
|
||
</table>
|
||
|
||
<a NAME="IEB_Research"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/IEB/Research/">R&D Projects</a> - The IEB Research
|
||
and
|
||
Development Area is a place for IEB projects and datasets which may never become
|
||
fully supported NCBI resources. This includes early prototypes of software,
|
||
results
|
||
of early or one-off analyses, tools that a fully functional but not integrated
|
||
into
|
||
the main, public NCBI systems, or datasets that may have some value but do not
|
||
fit
|
||
well into the main NCBI pages. </tr>
|
||
</table>
|
||
|
||
<a NAME="ASN.1"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="Summary/asn1.html">ASN.1</a> - The software in the <a
|
||
href="/IEB/ToolBox/">NCBI ToolBox</a> is primarily designed to read Abstract
|
||
Syntax
|
||
Notation 1 (ASN.1) format records, an International Standards Organization (ISO)
|
||
data representation format. The readme files in the <a
|
||
href="ftp://ftp.ncbi.nih.gov/toolbox/">toolbox</a> and <a
|
||
href="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/">toolbox/ncbi_tools</a>
|
||
directories
|
||
of the FTP site contain more information about the toolbox and ASN.1. An <a
|
||
href="Summary/asn1.html">ASN.1 summary</a> is also available. The ToolBox can
|
||
produce data as either ASN.1, as before, or as XML (<a
|
||
href="/IEB/ToolBox/XML/ncbixml.txt">more about XML</a>). Additional information
|
||
about the ToolBox, documentation, and demo programs are available on the <a
|
||
href="/IEB/ToolBox/">NCBI ToolBox</a> page.</tr>
|
||
</table>
|
||
|
||
<a NAME="IEB_FTP"></a>
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/toolbox/">FTP NCBI Software
|
||
ToolBox</a> - set of software and data exchange specifications used by NCBI to
|
||
produce portable, modular software for molecular biology. The software in the
|
||
Toolbox is primarily designed to read ASN.1 format records. It is available to
|
||
the
|
||
public in the toolbox directory of NCBI's ftp site, and can be used in its own
|
||
right
|
||
or as a foundation for building tools with similar properties. The readme files
|
||
in
|
||
the <a href="ftp://ftp.ncbi.nih.gov/toolbox/">toolbox</a> and <a
|
||
href="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/">toolbox/ncbi_tools</a>
|
||
directories
|
||
contain more information about the toolbox and ASN.1. An <a
|
||
href="Summary/asn1.html">ASN.1 summary</a> is also available. The ToolBox can
|
||
produce data as either ASN.1, as before, or as XML (<a
|
||
href="/IEB/ToolBox/XML/ncbixml.txt">more about XML</a>). Additional information
|
||
about the ToolBox, documentation, and demo programs are available on the <a
|
||
href="/IEB/ToolBox/">NCBI ToolBox home page</a>. </tr>
|
||
</table -->
|
||
|
||
<p></p>
|
||
<!-- ===================== END SOFTWARE ENGINEERING ================ -->
|
||
|
||
|
||
<!-- ================ EDUCATION ========================= -->
|
||
<p>
|
||
<a NAME="Education"></a>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" CLASS="H3a">Education</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a
|
||
href="/Education/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="95%" BGCOLOR="#FFFFFF">
|
||
<blockquote>
|
||
<a href="#News">News</a>,
|
||
<a href="#EducationBooks">Books</a>,
|
||
<a href="#Glossaries">Glossaries</a>,
|
||
<a href="#Tutorials">Tutorials</a>,
|
||
<a href="#Courses">Courses</a>,
|
||
<a href="#AdditionalResources">Additional Resources</a>
|
||
</td>
|
||
<td CLASS="TEXT" WIDTH="5%" BGCOLOR="#FFFFFF"> </td>
|
||
</tr>
|
||
</table>
|
||
<br>
|
||
|
||
<!-- ======== CATEGORY WITHIN EDUCATION: NEWS ======== -->
|
||
|
||
<a NAME="News"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">News - keeping up with
|
||
the
|
||
changes at NCBI</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/Education/BLASTinfo/milestones.html">Bioinformatics</a> -
|
||
A brief introduction to some milestones in bioinformatics.</td>
|
||
</tr>
|
||
</table -->
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=newsncbi">NCBI News</a> -
|
||
announcements about new resources, enhancements to existing resources, staff publications,
|
||
tutorials, FAQs.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/whatsnew.html">What's New</a> - recently
|
||
released
|
||
resources and enhancements to existing resources</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="Summary/email_lists.html">NCBI Announcements Email
|
||
Lists</a> -
|
||
Receive announcements about changes and updates to a variety of NCBI services.
|
||
In addition to a general NCBI-announce list, topic-specific e-mail lists are
|
||
available for BLAST, GenBank, dbSNP, Genomes, LinkOut, RefSeq, Sequin, and Entrez
|
||
Utilities (for making WWW Links to Entrez). Information on <a
|
||
href="Summary/email_lists.html">how to subscribe</a> is provided.
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ======== CATEGORY WITHIN EDUCATION: BOOKS ======== -->
|
||
|
||
<a NAME="EducationBooks"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Books</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/books/bv.fcgi?call=bv.View..ShowTOC&rid=coffeebrk.TOC&depth=1">Coffee
|
||
Break</a> - a collection of short reports on recent biological discoveries. Each
|
||
report incorporates interactive tutorials that show how bioinformatics tools are
|
||
used as a part of the research process.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/books/bv.fcgi?rid=gnd">Genes and Disease</a> - introduction to the
|
||
relationship between genetic factors and human disease. Summary information for
|
||
~60 genetic diseases with links to related databases and organizations.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook.TOC&depth=2">NCBI
|
||
Handbook</a> - an online book, written by NCBI staff, that discusses
|
||
the many resources available at NCBI. Each chapter is
|
||
devoted to one service; after a brief overview on using
|
||
the resource, there is an account of how the resource works,
|
||
including topics such as how data are included in a database,
|
||
database design, query processing, and how the different
|
||
resources relate to each other.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/entrez/query.fcgi?db=books">Entrez Books</a> - In
|
||
collaboration with book publishers, the NCBI is adapting textbooks for the web
|
||
and
|
||
linking them to PubMed, the biomedical bibliographic database. The idea is to
|
||
provide background information to PubMed, so that users can explore unfamiliar
|
||
concepts found in PubMed search results.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
|
||
<!-- ======== CATEGORY WITHIN EDUCATION: GLOSSARIES ======== -->
|
||
|
||
<a NAME="Glossaries"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Glossaries</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/books/bv.fcgi?call=bv.View..ShowSection&rid=handbook.glossary.1237">NCBI
|
||
Handbook Glossary</a> - part of the NCBI Handbook, described <a
|
||
href="#NCBIHandbook">above</a>. Includes a variety of terms pertaining to
|
||
biological data and bioinformatics.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Class/FieldGuide/glossary.html">FieldGuide
|
||
Glossary</a> -
|
||
developed for the Field Guide course described <a
|
||
href="#Courses">below</a>.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/genome/glossary.htm">Genome Glossary</a> -
|
||
commonly used genome terms; includes links to associated literature for each
|
||
term.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="/genome/guide/build.html#glossary">Human Genome
|
||
Build
|
||
Glossary</a> - accompanies the document that describes the <a
|
||
href="/genome/guide/build.html">NCBI Genomic Sequence Assembly and Annotation
|
||
Process</a>.<ul></td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><a href="/genome/guide/mouse/glossary.htm">Mouse Genome Build
|
||
Glossary</a> - accompanies the <a href="/genome/guide/mouse/mm_build.html">NCBI
|
||
Mouse Contig Assembly and Annotation Process</a>.</td>
|
||
</tr -->
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://www.genome.gov/page.cfm?pageID=10002096">NHGRI
|
||
Talking Glossary of Genetic Terms</a> - by the National Human Genome Research
|
||
Institute (NHGRI).</td>
|
||
</tr>
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ======== CATEGORY WITHIN EDUCATION: TUTORIALS ======== -->
|
||
|
||
<a NAME="Tutorials"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td CLASS="TEXT" WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Tutorials</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/bookshelf/br.fcgi?book=comgen&part=blast">BLAST QuickStart: Example-Driven Web-Based
|
||
BLAST Tutorial</a> - a tutorial based on the former NCBI minicourse, "BLAST Quick Start", within the
|
||
Comparative Genomics online book.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/bookshelf/br.fcgi?book=comgen&part=psibl">PSI-BLAST Tutorial</a> - a chapter
|
||
within the Comparative Genomics online book.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/bookshelf/br.fcgi?book=comgen&part=gene">Identification of Disease Genes:
|
||
Example-Driven Web-Based Tutorial</a> - a tutorial based on the former NCBI minicourse, "Identification of
|
||
Disease Genes", within the Comparative Genomics online book.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="SciencePrimer"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/About/primer/index.html">Science Primer</a> - The
|
||
science
|
||
behind our resources. An introduction for researchers, educators and the public.
|
||
Provides a plain language introductions to bioinformatics, genome mapping,
|
||
molecular
|
||
modeling, SNPs, ESTs, microarray technology, molecular genetics,
|
||
pharmacogenomics,
|
||
and phylogenetics.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="http://www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.html">PubMed Tutorial</a>
|
||
-
|
||
comprehensive instruction on using PubMed's various features <!--and<br> <a
|
||
href="/Literature/pubmed_search.html">PubMed Tour</a> (brief introduction
|
||
illustrating how to do a simple search) --></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Entrez/tutor.html">Entrez Tutorial</a> - show users
|
||
how
|
||
to make use of the full power of the Entrez data retrieval system. Using a human
|
||
gene as an example, it demonstrates the variety of information that can be
|
||
gathered
|
||
for a single gene across a number of Entrez databases.</td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><a href="/Database/tut1.html">Entrez Nucleotides
|
||
Tutorial</a></td>
|
||
</tr -->
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><a href="/Literature/omim_search.html">OMIM Tutorial</a></td>
|
||
</tr -->
|
||
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/BLAST/tutorial/Altschul-1.html">BLAST
|
||
Statistics</a></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Structure/CN3D/cn3dtut.shtml">3-D Protein Structure
|
||
Tutorial: Cn3D structure viewing program</a><SPACER TYPE=vertical
|
||
SIZE="5"></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/books/bv.fcgi?rid=handbook.chapter.ch24">Map Viewer
|
||
Exercises</a> - a chapter within the <a
|
||
href="/books/bv.fcgi?call=bv.View..ShowSection&rid=handbook">NCBI Handbook</a>
|
||
(described <a href="#NCBIHandbook">above</a>).<SPACER TYPE=vertical
|
||
SIZE="5"></td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<a NAME="CoffeeBreak"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="/books/bv.fcgi?call=bv.View..ShowSection&rid=coffeebrk">Coffee
|
||
Break</a> - a collection of short reports on recent biological discoveries. Each
|
||
report incorporates interactive tutorials that show how bioinformatics tools are
|
||
used as a part of the research process.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ======== CATEGORY WITHIN EDUCATION: COURSES ======== -->
|
||
|
||
<a NAME="Courses"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Courses</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="/Education/index.html">Education</a> - for information on past NCBI courses, please see the
|
||
Education home page.
|
||
</td>
|
||
</tr>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><FONT color="336699">Getting Started with Linkout</FONT> -
|
||
LinkOut is a feature of PubMed that provides users with links from PubMed
|
||
and other Entrez databases to a wide variety of relevant web-accessible
|
||
online resources, including full-text publications, biological databases,
|
||
consumer health information, research tools, and more. The goal is to
|
||
facilitate access to relevant online resources beyond the Entrez system to
|
||
extend, clarify, or supplement information found in the Entrez database.
|
||
|
||
This hands-on class is designed to introduce students to LinkOut and provide
|
||
step-by-step instruction on activating LinkOut for print and electronic
|
||
journal collections, allowing users to see their own library's holdings and
|
||
access electronic full-text through the PubMed interface. Topics covered are
|
||
registration for LinkOut, entering holdings, displaying a library's icon for
|
||
"branding" purposes, and access to free full-text through LinkOut.
|
||
Getting Started with LinkOut is a free class and is awarded 4 MLA continuing
|
||
education credits. For more information and to register, visit the NLM's National
|
||
Training Center and Clearinghouse (NTCC) website:
|
||
<a href="http://nnlm.gov/mar/online/">http://nnlm.gov/mar/online/</a>.
|
||
|
||
Questions about the class can be sent to <a
|
||
href="mailto:lib-linkout@ncbi.nlm.nih.gov">lib-linkout@ncbi.nlm.nih.gov</a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><a href="http://bimas.cit.nih.gov/linkage/index.html">Genetic
|
||
Linkage Analysis</a></td>
|
||
</tr -->
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><a href="http://www.nhgri.nih.gov/COURSE2000/">NHGRI Current
|
||
Topics
|
||
in Genome Analysis</a> - <a href="http://www.nhgri.nih.gov/COURSE2002/">Fall
|
||
2002</a> (handouts available on web) <!-- a
|
||
href="http://www.nhgri.nih.gov/COURSE99/">Spring 1999</a> (lectures and handouts
|
||
available on web) --></td>
|
||
</tr -->
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT">Smithsonian Institution and NHGRI Campus on the Mall (Winter
|
||
2001)
|
||
presents: "<a href="http://www.nhgri.nih.gov/CONF/SI/">The Human Genome Project:
|
||
From Maps to Medicine</a>"</td>
|
||
</tr -->
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ========CATEGORY WITHIN EDUCATION: ADDITIONAL RESOURCES======== -->
|
||
|
||
<a NAME="AdditionalResources"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Additional Resources</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://cancer.gov/cancerinformation/">Cancer
|
||
Information</a> - a wide range of accurate, credible cancer information brought
|
||
to
|
||
you by the National Cancer Institute (NCI). CancerNet information is reviewed
|
||
regularly by oncology experts and is based on the latest research. It includes
|
||
information selected and organized for patients, health professionals, and basic
|
||
researchers.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://www.genome.gov/Research/">Human Genome
|
||
Project</a>
|
||
- an international research effort to characterize the genomes of human and
|
||
selected
|
||
model organisms through complete mapping and sequencing of their DNA; to develop
|
||
technologies for genomic analysis; to examine the ethical, legal, and social
|
||
implications of human genetics research; and to train scientists who will be
|
||
able to
|
||
utilize the tools and resources developed through the HGP to pursue biological
|
||
studies that will improve human health. This link leads to the information
|
||
provided
|
||
on the <a href="http://www.genome.gov/">National Human Genome Research Institute
|
||
(NHGRI)</a> web site.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://www.genome.gov/Education/">NHGRI Educational
|
||
Resources</a> - the National Human Genome Research Institute (NHGRI) provides a
|
||
range of educational resources, including glossaries, fact sheets, multimedia
|
||
educational kits, genetic education modules for use by teachers, and a variety
|
||
of
|
||
online materials.</td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><a href="http://www.genome.gov/Careers/">NHGRI Careers and
|
||
Training</a> - describes education, training, and professional development
|
||
programs
|
||
at the National Human Genome Research Institute (NHGRI).</td>
|
||
</tr -->
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="http://science-education.nih.gov/homepage.nsf">NIH
|
||
Office
|
||
of Science Education</a> - offers a wide variety of educational resources for students at various grade levels, teachers, and the general public. Resources cover a wide range of topics, including Genetics, and formats of educational materials range from lesson plans and curricula to multimedia, online materials, and more. Website also includes a section on career exploration.</td>
|
||
</tr>
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://science-education.nih.gov/Homepage.nsf/for+teachers?OpenForm">For
|
||
Teachers</a> <!-- - see <a
|
||
href="http://science-education.nih.gov/Homepage.nsf/menu?openform&ParentUNID=B12
|
||
6D47
|
||
047197EE68525658D00081276">educational resources</a>/<a
|
||
href="http://science-education.nih.gov/Homepage.nsf/menu?openform&ParentUNID=82D
|
||
60BF
|
||
825A3A55E852566F80050B84F">genetics learning tools</a --></ul></td>
|
||
</tr -->
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://science-education.nih.gov/Homepage.nsf/for+students?OpenForm">For
|
||
Students</a> <!-- - see <a
|
||
href="http://science-education.nih.gov/Homepage.nsf/menu?openform&ParentUNID=883
|
||
668D
|
||
EFFC4A338852565F60073195E">learn about science and medicine</a>/<a
|
||
href="http://science-education.nih.gov/Homepage.nsf/menu?openform&ParentUNID=C74
|
||
F69F
|
||
EE01D4222852566F2006ED1DA">genetics</a --></ul></td>
|
||
</tr -->
|
||
|
||
<!-- tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="http://science-education.nih.gov/Homepage.nsf/for+the+public?OpenForm">For
|
||
the
|
||
Public</a> <!-- - see also <a href="http://health.nih.gov/">NIH Health
|
||
Information
|
||
Index</a --></ul></td>
|
||
</tr -->
|
||
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- =========================END_EDUCATION======================== -->
|
||
|
||
|
||
<!-- =============================FTP_SITE========================= -->
|
||
<a NAME="FTPSite"></a>
|
||
<p>
|
||
<table BORDER="0" CELLSPACING="0" CELLPADDING="3" WIDTH="98%">
|
||
<tr>
|
||
<td WIDTH="83%" BGCOLOR="#6699CC" CLASS="H3a">FTP Site</td>
|
||
<td WIDTH="13%" BGCOLOR="#6699CC" CLASS="H4a"><a
|
||
href="/Ftp/index.html">Overview</a></td>
|
||
<td WIDTH="3%" BGCOLOR="#6699CC" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup_white.gif" border="0" width="14" height="14"
|
||
ALT="back to top"></a></td>
|
||
</tr>
|
||
</table>
|
||
</p>
|
||
|
||
<!-- ========CATEGORY WITHIN FTP_SITE: DATABASES======== -->
|
||
|
||
<a NAME="FTPDatabases"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Download Databases</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/blast/db/">BLAST databases</a>
|
||
- a
|
||
collection of databases formatted for use with the BLAST software. A <a
|
||
href="ftp://ftp.ncbi.nih.gov/blast/db/README">readme</a> file provides database
|
||
descriptions.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="FTP_GenBank"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT">GenBank and Daily Updates</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="ftp://ftp.ncbi.nih.gov/genbank/">GenBank flat
|
||
file
|
||
format</a> - see <a href="samplerecord.html">sample GenBank record</a> and
|
||
detailed
|
||
description in <a href=ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt>GenBank release
|
||
notes</a>; download most recent <b>full release</b> (described <a
|
||
href="#Overview">above</a>) and <b>daily cumulative or non-cumulative update</b>
|
||
files</ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="ftp://ftp.ncbi.nih.gov/ncbi-asn1/">ASN.1
|
||
format</a> - Abstract Syntax Notation 1, an International Standards Organization
|
||
(ISO) data representation format; download most recent full release (described
|
||
<a
|
||
href="#Overview">above</a>) and daily cumulative or non-cumulative update files.
|
||
(<a href="Summary/asn1.html">more on ASN.1</a>)</ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="ftp://ftp.ncbi.nih.gov/blast/db/FASTA/">FASTA
|
||
format</a> - definition line followed by sequence data only (<a
|
||
href="/BLAST/fasta.html">example</a>). The FASTA formatted data are available
|
||
in
|
||
the BLAST databases directory of the FTP site. A <a
|
||
href="ftp://ftp.ncbi.nih.gov/blast/db/README">readme</a> file in that directory
|
||
provides descriptions of the available data sets, such as <b>nt.Z</b> (daily
|
||
updated
|
||
non-redundant BLAST nucleotide database, contains GenBank+EMBL+DDBJ+PDB
|
||
sequences,
|
||
but no EST, STS, GSS, or HTGS sequences), <b>nr.Z</b> (daily updated
|
||
non-redundant
|
||
proteins), <b>est.Z</b>, <b>gss.Z</b>, <b>htg.Z</b>, <b>sts.Z</b>, and
|
||
others.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/refseq/">RefSeq</a> - NCBI
|
||
database
|
||
of Reference Sequences. Curated, non-redundant set including genomic DNA
|
||
contigs,
|
||
mRNAs and proteins for known genes, mRNAs and proteins for gene models, and
|
||
entire
|
||
chromosomes. Accession numbers have the format of two letters, an underscore
|
||
bar,
|
||
and six digits, for example: NT_123456, NM_123456, NP_123456, NC_123456,
|
||
NG_123456, XM_123456, XR_123456, XP_123456 (more info about <a
|
||
href="/RefSeq/key.html#accession">accession numbers</a> and <a
|
||
href="/RefSeq/RSfaq.html#access">access</a>).</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a
|
||
href="ftp://ftp.ncbi.nlm.nih.gov/gene/">Entrez Gene</a> -
|
||
a collection of files from the Entrez Gene database, which is <a
|
||
href="#EntrezGene">described</a> in the Molecular Databases/Genes section of this
|
||
guide.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/snp/">dbSNP</a> - database of
|
||
single nucleotide polymorphisms, small-scale insertions/deletions, polymorphic
|
||
repetitive elements, and microsatellite variation<SPACER TYPE=vertical
|
||
SIZE="10"></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/pub/taxonomy/">Taxonomy</a> -
|
||
data
|
||
from the NCBI Taxonomy database (described <a href="#Taxonomy">above</a>).
|
||
Includes
|
||
a UNIX compressed tar file called "taxdump.tar.Z" that is updated daily and
|
||
contains
|
||
a dump of the taxonomy information from SyBase. Note that the *.dmp files are
|
||
not
|
||
human-friendly files, but can be uploaded into SyBase with the
|
||
BCP facility. When you uncompress and untar the file, you will see several
|
||
files,
|
||
including a Readme file that contains more information.</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/repository/">Repository of
|
||
databases</a> - This FTP directory contains a mix of NCBI databases (e.g.,
|
||
UniGene,
|
||
GeneMap, dbEST, dbGSS, dbSTS, OMIM) and a number of externally developed
|
||
databases
|
||
(e.g., EPD, TFD). The external databases are made available on the FTP site as
|
||
a
|
||
service to the scientific community. They are contributed by outside scientists
|
||
and
|
||
maintained independently of NCBI. All the files in the FTP directory of a
|
||
non-NCBI
|
||
database are placed there and maintained by the developers of that database.
|
||
Questions about non-NCBI databases should be directed to the contacts listed in
|
||
the
|
||
readme or other background files for the individual databases. Note that
|
||
additional
|
||
NCBI databases are also found in the <a href="ftp://ftp.ncbi.nih.gov/">root
|
||
directory</a> of the FTP site (under the database name, such as GenBank, Gene,
|
||
RefSeq), or in the <a href="ftp://ftp.ncbi.nih.gov/pub/">"pub" directory</a>
|
||
(usually under the name of the primary resource developer).</td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
|
||
<!-- ======== CATEGORY WITHIN FTP_SITE: GENOMES ======== -->
|
||
|
||
<a NAME="FTP_Genomes"></a>
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Download Genomes</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
<p></p>
|
||
<!-- ======== HUMAN_GENOME_PROJECT_FTP_DATA ======== -->
|
||
|
||
<a NAME="FTP_HumanGenome"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/"><b>Human
|
||
Genome
|
||
Project Data</b></a> - the <a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/">ftp://ftp.ncbi.nih.gov/genomes/
|
||
H_sa
|
||
piens/</a> directory contains one folder for each chromosome, which includes
|
||
genomic
|
||
contigs (NT_* records) built from finished and unfinished sequence data. The
|
||
contigs are available in various formats, described below. The <a
|
||
href="/genome/guide/build.html">contig assembly and annotation process</a> is
|
||
described in a separate document.
|
||
|
||
<table border="0" cellpadding="0">
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.asn</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">ASN.1 format (description <a
|
||
href="#ASN1">above</a>)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.fa.gz</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">FASTA format (description <a
|
||
href="#FASTA">above</a>)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.gbk.gz</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">GenBank flat file format<br>
|
||
(annotations currently include STS markers; known and
|
||
predicted genes will be added in coming months)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.gbs</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">GenBank summary format<br>
|
||
(this format does not contain sequence data, but instead
|
||
contains a "CONTIG" field, showing how the contig is assembled
|
||
from individual GenBank accessions)</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT" width="21%" valign="top">hs_chr*.mfa.gz</td>
|
||
<td CLASS="TEXT" width="79%" valign="top">masked FASTA format (masked
|
||
nucleotides
|
||
are lower case)</td>
|
||
</tr>
|
||
</table>
|
||
|
||
Data from the Map Viewer (described <a
|
||
href="#HumanChromosomeMapViews">above)</a>
|
||
are available in the <a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/maps/mapview/">ftp://ftp.ncbi.nih
|
||
.gov
|
||
/genomes/H_sapiens/maps/mapview/</a> subdirectory.
|
||
<SPACER TYPE=vertical SIZE="10">
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
<!-- ======== END_HUMAN_GENOME_PROJECT_FTP_DATA ======== -->
|
||
|
||
<!-- ======== OTHER_GENOMES_FTP_DATA ======== -->
|
||
|
||
<a NAME="FTP_OtherGenomes"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT">
|
||
<FONT CLASS="H3">Other Genomes</FONT> - such as bacteria, nematode, mouse, and
|
||
others can be downloaded from one of two directories:
|
||
<ul>
|
||
<li><a
|
||
href="ftp://ftp.ncbi.nih.gov/genomes/">ftp://ftp.ncbi.nih.gov/genomes/</a> -
|
||
designed to contain genomes assembled and/or curated at NCBI. These genomes are
|
||
part of the <b>RefSeq</b> database, described <a href="#RefSeq">above</a>.
|
||
<li><a
|
||
href="ftp://ftp.ncbi.nih.gov/genbank/genomes/">ftp://ftp.ncbi.nih.gov/genbank/ge
|
||
nome
|
||
s/</a> - designed to contain complete genomes submitted in their entirety to
|
||
<b>GenBank</b>
|
||
</ul>
|
||
<blockquote><i>Note:</i> In some cases, an organism might be listed in both
|
||
directories. This can happen for several reasons: (1) there are two versions of
|
||
the
|
||
genome are available - one in GenBank, and one in RefSeq; or (2) the organism's
|
||
data
|
||
was assembled at NCBI and was available from the "/genbank/genomes/" directory
|
||
before the new "/genomes/" directory was set up. In the latter case, the data
|
||
now
|
||
exists in the new "/genomes/" directory, but a symbolic link was preserved in
|
||
the
|
||
original directory to facilitate user access.</blockquote>
|
||
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
|
||
<!-- ======== END_OTHER_GENOMES_FTP_DATA ======== -->
|
||
|
||
<!-- ================CATEGORY WITHIN FTP_SITE: SOFTWARE================ -->
|
||
|
||
<a NAME="FTPSoftware"></a>
|
||
|
||
<table BORDER="0" WIDTH="91%" CELLSPACING="0" BGCOLOR="#e0eeee">
|
||
<tr>
|
||
<td WIDTH="96%" BGCOLOR="#e0eeee" class="H3">Download Software</td>
|
||
<td WIDTH="4%" BGCOLOR="#e0eeee" VALIGN="top" ALIGN="center">
|
||
<a href="#Top"><img SRC="arrowup.gif" border="0" width="14" height="14"
|
||
ALT="back to
|
||
top"></a></td>
|
||
</tr>
|
||
</table>
|
||
|
||
<a NAME="FTP_BLAST"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="H3">BLAST Programs</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST-BLAST/">BLAST
|
||
Stand-Alone
|
||
Program</a> - a set of executables which are <b>run by command line</b>.
|
||
Binaries
|
||
are provided for IRIX 6.2, Solaris 2.6, DEC OSF1 (ver. 4.0d), LINUX, and Win32
|
||
systems. Please read the <a
|
||
href="ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blast.txt">README</a> for more
|
||
information. There is also some
|
||
information on setting up Standalone BLAST at the NHGRI site at
|
||
<a
|
||
href="http://genome.nhgri.nih.gov/blastall/blast_install/">http://genome.nhgri.n
|
||
ih.g
|
||
ov/blastall/blast_install/</a>.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST-WWWBLAST">BLAST Web
|
||
Server
|
||
Program</a> - allows you to set up your own <b>in-house version of the NCBI
|
||
BLAST
|
||
web pages</b> on a UNIX web server. You can set up the program to search your
|
||
own
|
||
custom databases or downloaded copies of the NCBI databases. This server is not
|
||
intended to handle the large loads which may exist in public service settings.
|
||
A <a
|
||
href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST-WWWBLAST/readme.html">
|
||
Read
|
||
me</a> file provides more information.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST-NETBLAST/">Network
|
||
BLAST</a> - a TCP/IP-based client-server version of WWW Gapped BLAST (2.0).
|
||
Makes a
|
||
direct connection with the NCBI databases over the Internet to retrieve data.
|
||
Client
|
||
software is available for PC, Mac, and Unix. For general information about
|
||
Gapped
|
||
BLAST, see <a href="#BLAST">above<a/>.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><blockquote><b>NOTE:</b> <i><a
|
||
href="ftp://ftp.ncbi.nih.gov/blast/db/">Preformatted BLAST databases</a> also
|
||
available for downloading, in addition to the software listed above. A <a
|
||
href="ftp://ftp.ncbi.nih.gov/blast/db/README">readme</a> file provides database
|
||
descriptions.</i></blockquote></td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td CLASS="H3">Client/server programs</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="ftp://ftp.ncbi.nih.gov/sequin/">Sequin</a> -
|
||
submission software program for one or many submissions, long sequences,
|
||
complete
|
||
genomes, alignments, population/ phylogenetic/ mutation studies. Can be used as
|
||
a
|
||
stand-alone application or in a TCP/IP-based "network aware" mode, with links to
|
||
other NCBI resources and software such as <a
|
||
href="#Entrez">Entrez</a>.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a href="ftp://ftp.ncbi.nih.gov/entrez/">Network
|
||
Entrez</a>
|
||
- a TCP/IP-based client-server version of WWW Entrez. Makes a direct connection
|
||
with
|
||
the NCBI databases over the Internet to retrieve data. Client software is
|
||
available
|
||
for PC, Mac, and Unix. For general information about Entrez, see <a
|
||
href="#Entrez">above<a/>.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><ul><li><a
|
||
href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST-NETBLAST/">Network
|
||
BLAST</a> - see description <a href="#FTP_BLAST">above<a/>.</li></ul></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/cn3d/">Cn3D</a> - "See in 3-D,"
|
||
a
|
||
structure and sequence alignment viewer for NCBI databases. It allows viewing
|
||
of
|
||
3-D structures and sequence-structure or structure-structure alignments. Cn3D
|
||
can
|
||
work as a helper application to your browser, or as a client-server application
|
||
that
|
||
retrieves structure records from MMDB (described <a href="#MMDB">above</a>)
|
||
directly
|
||
over the internet. The <a href="/Structure/CN3D/cn3d.shtml">Cn3D home page</a>
|
||
provides access to information on how to <a
|
||
href="/Structure/CN3D/cn3dinstall.shtml">install</a> the program, a <a
|
||
href="/Structure/CN3D/cn3dtut.shtml">tutorial</a> to get started, and a
|
||
comprehensive <a href="/Structure/CN3D/cn3dhelp.shtml">help document</a>.</td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<a NAME="FTP_ToolBox"></a>
|
||
<table BORDER="0" CELLSPACING="5" WIDTH="90%" BGCOLOR="#FFFFFF">
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/toolbox/">NCBI Software
|
||
ToolBox</a>
|
||
- set of software and data exchange specifications used by NCBI to produce
|
||
portable,
|
||
modular software for molecular biology. The software in the Toolbox is
|
||
primarily
|
||
designed to read Abstract Syntax Notation 1 (ASN.1) format records, an
|
||
International
|
||
Standards Organization (ISO) data representation format. The software is
|
||
available
|
||
to the public in the toolbox/ncbi_tools directory of NCBI's ftp site, and can be
|
||
used in its own right or as a foundation for building tools with similar
|
||
properties.
|
||
The readme files in the <a href="ftp://ftp.ncbi.nih.gov/toolbox/">toolbox</a>
|
||
and
|
||
<a href="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/">toolbox/ncbi_tools</a>
|
||
directories of the FTP site contain more information about the toolbox and
|
||
ASN.1.
|
||
An <a href="Summary/asn1.html">ASN.1 summary</a> is also available. The
|
||
ToolBox
|
||
can produce data as either ASN.1, as before, or as XML (<a
|
||
href="/IEB/ToolBox/XML/ncbixml.txt">more about XML</a>). Additional information
|
||
about the ToolBox, documentation, and demo programs are available on the <a
|
||
href="/IEB/ToolBox/">NCBI ToolBox</a> page. Additional information about the
|
||
Information Engineering Branch (IEB) of NCBI, which develops the ToolBox, is
|
||
provided <a href="#SoftwareEngineering">above</a>, along with other items of
|
||
interest to software developers.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td CLASS="TEXT"><a href="ftp://ftp.ncbi.nih.gov/pub/">Software programs
|
||
developed
|
||
as personal projects by various NCBI scientists</a> - /pub directory of FTP site
|
||
contains programs such as MACAW (multiple sequence alignments) and e-PCR
|
||
(description <a href="#ePCR">above</a>).</td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
<p></p>
|
||
|
||
<!-- ===============================END_FTP_SITE===================== -->
|
||
|
||
|
||
<!-- ============PLACE_EXTRA_TITLE_BARS_ABOVE_HERE================ -->
|
||
|
||
<!-- ===================END_OF_CONTENT============================ -->
|
||
|
||
<table BORDER=0 CELLSPACING=0 CELLPADDING=3 WIDTH="100%" BGCOLOR="#003366" >
|
||
<tr ALIGN=CENTER>
|
||
|
||
<td WIDTH="20%"><a href="mailto:info@ncbi.nlm.nih.gov" class="BAR">Help
|
||
Desk</a></td>
|
||
|
||
<td WIDTH="20%"><a href="http://www.ncbi.nlm.nih.gov" class="BAR">NCBI</a></td>
|
||
|
||
<td WIDTH="20%"><a href="http://www.nlm.nih.gov" class="BAR">NLM</a></td>
|
||
|
||
<td WIDTH="20%"><a href="http://www.nih.gov" class="BAR">NIH</a></td>
|
||
|
||
<td WIDTH="20%"><a href="credits.html" class="BAR">Credits</a></td>
|
||
|
||
</tr>
|
||
</table>
|
||
|
||
<table BORDER=0 CELLSPACING=0 CELLPADDING=3 WIDTH="100%" BGCOLOR="#FFFFFF" >
|
||
<tr>
|
||
<td CLASS="TEXT2">
|
||
<p><i><FONT size="2">Revised: February 3, 2009.</FONT></i><br>
|
||
<FONT size="2"><i>Questions about NCBI resources to</i> <a
|
||
href="mailto:info@ncbi.nlm.nih.gov">info@ncbi.nlm.nih.gov</a></FONT><br>
|
||
<p><FONT size="2"><a href="/About/disclaimer.html">Disclaimer</a></FONT>
|
||
<FONT size="2"><a
|
||
href="http://www.nlm.nih.gov/privacy.html">Privacy statement</a></FONT></p>
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</td>
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</tr>
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</table>
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</body>
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</html>
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