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yet</button><a id="jr-fip-next" class="wsprkl btn" title="Jump to next match">▶</a></nav></nav></div><div id="jr-epub-interstitial" class="hidden"></div><div id="jr-content"><article data-type="main"><div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><div class="fm-sec"><h1 id="_NBK6632_"><span class="title" itemprop="name">NCBI News, May 2009</span></h1><p class="contribs">Cooper P, Lipshultz D.</p><p class="fm-aai"><a href="#_NBK6632_pubdet_">Publication Details</a></p><p><em>Estimated reading time: 8 minutes</em></p></div></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="JEKOtU220.Featured1_1"><h2 id="_JEKOtU220_Featured1_1_">Featured Data: 2009 H1N1 Influenza Sequences</h2><p>NCBI is the repository for the 2009 influenza virus sequences from the global H1N1
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outbreak and is making every effort to make the sequences available as soon as
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possible. You can access the recent flu sequences and retrieve them individually
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from a special influenza virus resource page that is updated daily:</p><p>
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<a href="/genomes/FLU/SwineFlu.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html</a>
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</p><p>
|
|
<span class="graphic"><img src="/books/NBK6632/bin/may09image1.jpg" alt="may09.G1.png" /></span>
|
|
</p><div id="JEKOtU220.UsingFlu2_2"><h3>Using Flu Database Query Builder to Download Sequences in FASTA Format</h3><p>An easy way to get these sequences all at once is through the query builder on
|
|
the influenza virus database search page:</p><p>
|
|
<a href="/genomes/FLU/Database/select.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/genomes/FLU/Database/select.cgi</a>
|
|
</p><p>On this page you can select the characteristics of the flu sequences of interest
|
|
and then retrieve them or perform additional analyses such as multiple
|
|
alignments and phylogenetic tree construction. </p><p>
|
|
<span class="graphic"><img src="/books/NBK6632/bin/may09image2.jpg" alt="may09.G2.png" /></span>
|
|
</p><p>To get all of the recent H1N1 nucleotide sequences, select the nucleotide radio
|
|
button on the “show” line of the form, set the species
|
|
to “Influenzavirus A”, the host to
|
|
“human”, the Country/Region to
|
|
“any”, the collection date range to
|
|
“2009/04:2009/05”, and the subtype to
|
|
“H1N1”. Set the viral segment to
|
|
“any” to get all segments, or select a specific segment
|
|
or protein if desired. Click the “Get sequences” button
|
|
to list the matching sequences. This search retrieves 304 records at the time of
|
|
writing (May 7, 2009). </p><p>To download sequences in FASTA format choose the type of sequence desired
|
|
– protein, coding region, nucleotide – from the
|
|
“Select FASTA sequence for download” device at the top
|
|
of the page. The file download dialog box appears that allows saving all
|
|
sequences in FASTA format to a local file. </p><p>
|
|
<span class="graphic"><img src="/books/NBK6632/bin/may09image3.jpg" alt="may09.G3.png" /></span>
|
|
</p></div><div id="JEKOtU220.UsingBat3_2"><h3>Using Batch Entrez to Download GenBank and Other Formats</h3><p>Batch Entrez can be used to get the full records (GenBank, XML, or ASN.1) instead
|
|
of the FASTA format for the flu sequences. To do this, download the list of
|
|
accession numbers from the Flu database directly from the query builder results
|
|
obtained above by selecting the desired sequence (protein or nucleotide) from
|
|
the “Select accession list to download” device at the
|
|
top of the results page. Save the list to a local file. Then upload these using
|
|
the batch Entrez service to obtain the records as follows. Access the batch
|
|
Entrez page.</p><p>
|
|
<a href="/sites/batchentrez" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/sites/batchentrez</a>
|
|
</p><p>Click the “Browse” button at the top of the batch Entrez
|
|
page and point to the file containing the downloaded list of accessions. Click
|
|
the “Retrieve” button then the link in the results to
|
|
retrieve the influenza virus records in the Entrez nucleotide database. Once the
|
|
records are in the Entrez Nucleotide service you can use the features of Entrez
|
|
such as History and Preview/Index to refine your results if desired. See the
|
|
Entrez help documentation for details.</p><p>
|
|
<a href="/bookshelf/br.fcgi?book=helpentrez" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpentrez</a>
|
|
</p><p>Click on individual records to in the results to view them in GenBank format or
|
|
use the “Display” pull-down list to choose the format of
|
|
interest and show all records. The records will be displayed 20 per page.
|
|
Download the entire set by choosing the File option from the “Send
|
|
to” pull-down list at the top of the first page of records. </p></div><div id="JEKOtU220.Obtainin4_2"><h3>Obtaining the eight diagnostic records</h3><p>The World Health Organization has identified the eight segments of the earliest
|
|
H1N1 isolate from California as diagnostic sequences for the new influenza virus
|
|
strain.</p><p>
|
|
<a href="http://www.who.int/csr/disease/swineflu/swineflu_genesequences_20090425.pdf" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.who.int/csr/disease/swineflu/swineflu_genesequences_20090425.pdf</a>
|
|
</p><p>These sequences correspond to GenBank accession numbers <a href="/nuccore/?term=FJ966079:FJ966086[pacc]" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=nuccore">FJ966079-FJ966086</a>
|
|
available in the Entrez nucleotide service.</p><p>
|
|
<a href="/sites/entrez?db=nuccore" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore</a>
|
|
</p><p>Use the following query to retrieve these eight segments directly.</p><p><a href="/nuccore/?term=FJ966079:FJ966086[pacc]" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=nuccore">FJ966079:FJ966086</a>[Accession]</p></div><div id="JEKOtU220.FluSeque5_2"><h3>Flu Sequence Updates</h3><p>NCBI is expecting new data on a daily basis as the outbreak continues. Check the
|
|
flu virus pages listed above for breaking news and new sequences.</p></div></div><div id="JEKOtU220.Featured6_1"><h2 id="_JEKOtU220_Featured6_1_">Featured Resource: Protein Multiple Alignment Tool Web Service</h2><p>NCBI will soon offer a Web multiple protein alignment service that uses the
|
|
Constraint-Based Multiple Alignment Tool (COBALT)<a class="bibr" href="#JEKOtU220.Pap07" rid="JEKOtU220.Pap07">(1)</a>. COBALT can align a set of provided sequences
|
|
or can be run as an extension to a Web BLAST search performing a multiple alignment
|
|
on the set of protein sequences collected from the original BLAST search. The Web
|
|
implementation of COBALT uses information from pairwise protein BLAST (blastp)
|
|
scores, Conserved Domain Database results, and Prosite pattern matches as
|
|
constraints in an initial pairwise alignment that is followed by a progressive
|
|
multiple sequence alignment. The results from COBALT can be used with the BLAST
|
|
treeview service to generate a phylogenetic tree from the multiple alignment. An
|
|
often-requested service, the addition of a multiple alignment greatly enhances the
|
|
suite of sequence analysis tools available at the NCBI and provides a new and
|
|
powerful extension to BLAST.</p><div id="JEKOtU220.RunningC7_2"><h3>Running COBALT on a Set of Sequences</h3><p>The Web interface to COBALT will be available from the BLAST homepage or directly
|
|
from the following URL:</p><p>
|
|
<a href="/tools/cobalt/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/tools/cobalt/</a>
|
|
</p><p>The basic COBALT interface shown in <a class="figpopup" href="/books/NBK6632/figure/JEKOtU220.may09fig1/?report=objectonly" target="object" rid-figpopup="figJEKOtU220may09fig1" rid-ob="figobJEKOtU220may09fig1">Figure 1 A</a> has the advanced parameters available
|
|
through a link that expands the form. Advanced parameters include gap open and
|
|
extend penalties and constraint and clustering parameters. The default values
|
|
for the constraint and clustering parameters have been optimized to give the
|
|
best alignment without undue sacrifice of speed. Generally, altering the default
|
|
constraints will degrade performance. Detailed information on the any of the
|
|
advanced parameters is available through help documentation linked to each
|
|
option. </p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figJEKOtU220may09fig1" co-legend-rid="figlgndJEKOtU220may09fig1"><a href="/books/NBK6632/figure/JEKOtU220.may09fig1/?report=objectonly" target="object" title="Figure 1" class="img_link icnblk_img figpopup" rid-figpopup="figJEKOtU220may09fig1" rid-ob="figobJEKOtU220may09fig1"><img class="small-thumb" src="/books/NBK6632/bin/may09image4.gif" src-large="/books/NBK6632/bin/may09image4.jpg" alt="Figure 1. COBALT interface and multiple alignments." /></a><div class="icnblk_cntnt" id="figlgndJEKOtU220may09fig1"><h4 id="JEKOtU220.may09fig1"><a href="/books/NBK6632/figure/JEKOtU220.may09fig1/?report=objectonly" target="object" rid-ob="figobJEKOtU220may09fig1">Figure 1</a></h4><p class="float-caption no_bottom_margin">COBALT interface and multiple alignments. A. The basic COBALT interface
|
|
with seven NCBI accessions from the Homologene cluster for ATP citrate
|
|
lyase (Homologene ID 854) B. A portion of the COBALT multiple alignment
|
|
showing the aberrant chimpanzee gene <a href="/books/NBK6632/figure/JEKOtU220.may09fig1/?report=objectonly" target="object" rid-ob="figobJEKOtU220may09fig1">(more...)</a></p></div></div><p>COBALT accepts protein sequences in FASTA format or NCBI identifiers as input.
|
|
<a class="figpopup" href="/books/NBK6632/figure/JEKOtU220.may09fig1/?report=objectonly" target="object" rid-figpopup="figJEKOtU220may09fig1" rid-ob="figobJEKOtU220may09fig1">Figure 1 B</a> shows a
|
|
portion of the COBALT alignment obtained using nine of the protein sequences
|
|
from the NCBI HomoloGene cluster for ATP citrate lyase (HomoloGene ID 854). The
|
|
alignment contains an anomalous predicted protein from chimpanzee (<a href="/protein/332847769/?report=GenPept" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=genpept">XP_511495</a>)
|
|
that is mis-spliced because of missing data in the genome. This sequence creates
|
|
large gaps in the multiple alignment that interrupt the conserved Citryl-Coa
|
|
lyase domain. One very useful feature of the Web interface to COBALT is the
|
|
ability to edit the sequence set and perform another alignment with the modified
|
|
set (<a class="figpopup" href="/books/NBK6632/figure/JEKOtU220.may09fig1/?report=objectonly" target="object" rid-figpopup="figJEKOtU220may09fig1" rid-ob="figobJEKOtU220may09fig1">Figure 1 C</a>). In this
|
|
case, un-checking the box next to the chimpanzee sequence and re-submitting the
|
|
set produces the improved alignment shown in <a class="figpopup" href="/books/NBK6632/figure/JEKOtU220.may09fig1/?report=objectonly" target="object" rid-figpopup="figJEKOtU220may09fig1" rid-ob="figobJEKOtU220may09fig1">Figure 1 D</a>. </p></div><div id="JEKOtU220.RunningC8_2"><h3>Running COBALT from Web BLAST Results</h3><p>COBALT can also be run from the results of any Web protein BLAST search by
|
|
clicking the “Multiple Alignment” link in the
|
|
“Other reports” line on the BLAST results. This provides
|
|
an easy way to collect homologs in a set of species and align them for
|
|
phylogenetic or other comparative study. The most useful sets of sequences for
|
|
these purposes come from searches with well-defined taxon-restricted databases.
|
|
For example, a BLAST search with the human prolactin reference sequence
|
|
(<a href="/protein/4506105/?report=GenPept" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=genpept">NP_000939</a>) can collect growth hormone family members from bony fishes for
|
|
building a multiple alignment and a gene tree. A BLAST search using the
|
|
following settings finds 13 full-length growth hormone homologs from four
|
|
species of fish: Database = Reference proteins (refseq_protein); Organism = bony
|
|
fishes; Entrez query = srcdb refseq known[properties]; Expect threshold = 1e-6.
|
|
The Entrez query limit eliminates proteins based entirely on gene predictions.
|
|
The Expect threshold helps restrict the set to only closely related proteins and
|
|
can be adjusted after expanding the “Algorithm
|
|
parameters” of the BLAST form. A COBALT alignment can be generated
|
|
by clicking the “Multiple alignment” link in the
|
|
“Other reports” line at the top of the Descriptions or
|
|
Alignments section of the BLAST results (<a class="figpopup" href="/books/NBK6632/figure/JEKOtU220.may09fig2/?report=objectonly" target="object" rid-figpopup="figJEKOtU220may09fig2" rid-ob="figobJEKOtU220may09fig2">Figure 2</a>, top panel). The COBALT results appear in a
|
|
new browser window when ready (<a class="figpopup" href="/books/NBK6632/figure/JEKOtU220.may09fig2/?report=objectonly" target="object" rid-figpopup="figJEKOtU220may09fig2" rid-ob="figobJEKOtU220may09fig2">Figure 2</a>, middle panel). </p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figJEKOtU220may09fig2" co-legend-rid="figlgndJEKOtU220may09fig2"><a href="/books/NBK6632/figure/JEKOtU220.may09fig2/?report=objectonly" target="object" title="Figure 2" class="img_link icnblk_img figpopup" rid-figpopup="figJEKOtU220may09fig2" rid-ob="figobJEKOtU220may09fig2"><img class="small-thumb" src="/books/NBK6632/bin/may09image5.gif" src-large="/books/NBK6632/bin/may09image5.jpg" alt="Figure 2. BLAST, COBALT results, and phylogenetic tree of growth hormone family members for NCBI RefSeq proteins from teleost fishes." /></a><div class="icnblk_cntnt" id="figlgndJEKOtU220may09fig2"><h4 id="JEKOtU220.may09fig2"><a href="/books/NBK6632/figure/JEKOtU220.may09fig2/?report=objectonly" target="object" rid-ob="figobJEKOtU220may09fig2">Figure 2</a></h4><p class="float-caption no_bottom_margin">BLAST, COBALT results, and phylogenetic tree of growth hormone family
|
|
members for NCBI RefSeq proteins from teleost fishes. The sequences were
|
|
collected by a BLAST search limited to NCBI known RefSeqs
|
|
(refseq_protein database, srcdb_refseq_known Entrez <a href="/books/NBK6632/figure/JEKOtU220.may09fig2/?report=objectonly" target="object" rid-ob="figobJEKOtU220may09fig2">(more...)</a></p></div></div></div><div id="JEKOtU220.Generati9_2"><h3>Generating a Phylogenetic Tree from COBALT Results</h3><p>A phylogenetic tree can be generated from any set of COBALT results by clicking
|
|
the “Phylogenetic tree” link at the top (<a class="figpopup" href="/books/NBK6632/figure/JEKOtU220.may09fig2/?report=objectonly" target="object" rid-figpopup="figJEKOtU220may09fig2" rid-ob="figobJEKOtU220may09fig2">Figure 2</a>, middle panel).
|
|
The tree is generated using the Treeview (<a href="/bookshelf/br.fcgi?book=newsncbi&part=newsarchive" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI News, Summer 2006</a>) feature of the BLAST Web service. This
|
|
tree is calculated from a global multiple sequence alignment and is therefore
|
|
more accurate than the Distance tree that can be generated from the BLAST
|
|
results. The tree view display has options for redrawing the tree in different
|
|
format, recalculating the distance metrics, downloading the tree in text
|
|
formats, and displaying and realigning sequences from any node. The tree
|
|
generated from a multiple alignment of the fish growth hormone family members
|
|
collected by the BLAST search with the human prolactin precursor is shown on the
|
|
bottom panel of <a href="#JEKOtU220.may09fig2">Figure
|
|
2</a>. The tree shows three distinct subfamilies: growth hormone, prolactin,
|
|
and the somatolactins. The latter are pituitary hormones apparently found only
|
|
in fishes<a class="bibr" href="#JEKOtU220.Kan96" rid="JEKOtU220.Kan96">(2)</a>.</p></div><div id="JEKOtU220.Retrievi10_2"><h3>Retrieving Previous COBALT Results</h3><p>COBALT results from the Web service are stored at NCBI and are available for
|
|
later retrieval in the same way as ordinary BLAST results. Recent COBALT results
|
|
are available through the “Recent Results” tab at top of
|
|
the COBALT submission or results pages. Like BLAST results COBALT results may be
|
|
retrieved up 36 hours from the time of the search using the Request Identifier
|
|
(RID) that uniquely identifies each set of results.</p></div><div id="JEKOtU220.Summarya11_2"><h3>Summary and Future Directions</h3><p>The COBALT multiple protein alignment tool expands the suite of sequence analysis
|
|
tools available at the NCBI and provides a single pathway now for collecting
|
|
related sequences using BLAST and then performing a rapid and accurate multiple
|
|
alignment. Moreover for the first time multiple alignments can be used directly
|
|
at the NCBI to generate and display phylogenetic trees making the NCBI Website a
|
|
comprehensive resource for analyzing protein relationships. Upcoming
|
|
improvements to the COBALT tool include the ability to re-format and download
|
|
alignments in various standard formats such as FASTA plus gap. This will allow
|
|
COBALT multiple alignments to be imported into other multiple alignmentprograms
|
|
and editors.</p></div></div><div id="JEKOtU220.NewDatab13_1"><h2 id="_JEKOtU220_NewDatab13_1_">New Databases and Tools</h2><div id="JEKOtU220.H1N1Swin14_2"><h3>H1N1 Influenza Resources</h3><p>NCBI has various resources available as described above. The Influenza Virus Resource has 34 H1N1 influenza sequences listed
|
|
on the following page: <a href="/genomes/FLU/SwineFlu.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html</a>. PubMed
|
|
contains recently added <a href="/pubmed?term=swine+AND+(flu+OR+influenza+OR+h1n1)+AND+%22last+1+year%22%5bedat%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">literature citations related to</a> the new strain of influenza. </p></div><div id="JEKOtU220.PeptideD15_2"><h3>Peptide Data Resource</h3><p>Peptidome is a new public repository that archives and distributes tandem mass
|
|
spectrometry peptide and protein identification data. Web-based interfaces are
|
|
available to browse and explore studies, peptides, and proteins. For more
|
|
information see the Peptidome web page: <a href="/projects/peptidome/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/projects/peptidome/</a>.</p></div><div id="JEKOtU220.GenomeBu16_2"><h3>Genome Build</h3><p>Build 1 of the <i>Vitis vinifera</i> (wine grape) genome is available
|
|
in the Genomes database and on the NCBI Map Viewer. The Map Viewer page is:
|
|
<a href="/mapview/map_search.cgi?taxid=29760" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=29760</a></p></div><div id="JEKOtU220.Bookshel17_2"><h3>Bookshelf</h3><p>The Bookshelf has added a new chapter to the <i>NCBI Help Manual</i>, GaP FAQ Archive. The Bookshelf website URL
|
|
is: <a href="/sites/entrez?db=Books" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/sites/entrez?db=Books</a></p></div><div id="JEKOtU220.Microbia18_2"><h3>Microbial Genomes</h3><p>Fifteen finished microbial genomes were released between March 24-April 29. The
|
|
original sequence data files submitted to GenBank/EMBL/DDBJ are available on the
|
|
FTP site: <a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">ftp.ncbi.nih.gov/genbank/genomes/Bacteria/</a>. The RefSeq
|
|
provisional versions of these genomes are also available: <a href="ftp://ftp.ncbi.nih.gov/genomes/Bacteria/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">ftp.ncbi.nih.gov/genomes/Bacteria/</a>.</p></div></div><div id="JEKOtU220.GenBankN19_1"><h2 id="_JEKOtU220_GenBankN19_1_">GenBank News</h2><p>GenBank release 171.0 is available via web and FTP. The current release includes
|
|
information available as of April 10, 2009. Release notes are available on the on
|
|
the NCBI ftp site: <a href="ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">ftp.ncbi.nih.gov/genbank/gbrel.txt</a></p><p>NCBI is considering ceasing support for index files, so affected users are encouraged
|
|
to read that section of the release notes and provide feedback to the GenBank group.
|
|
</p></div><div id="JEKOtU220.Updatesa20_1"><h2 id="_JEKOtU220_Updatesa20_1_">Updates and Enhancements</h2><div id="JEKOtU220.SRATrans21_2"><h3>SRA Transcript BLAST</h3><p>SRA transcript sequences are now searchable through a specialized BLAST page. All
|
|
transcript sequences derived from 454 sequencing are available from
|
|
NCBI’s SRA database. To perform a search, go to <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">the SRA BLAST page</a>.</p></div><div id="JEKOtU220.GEODataS22_2"><h3>GEO DataSet Browser</h3><p>A new GEO DataSet Browser is available for browsing the curated gene expression
|
|
DataSets. The new tool is located: <a href="/sites/GDSbrowser" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/sites/GDSbrowser</a>.</p></div><div id="JEKOtU220.Sequence23_2"><h3>Sequence Analysis Tools Links in Entrez Sequence Databases</h3><p>A new Sequence Analysis Tools section is available on the right hand Discovery
|
|
column of Nucleotide and Protein records in the Entrez system. Sequence Analysis
|
|
Tools contains links to the BLAST service for both protein and nucleotide
|
|
sequences. Nucleotide records also link to Primer BLAST service. Both of these
|
|
links load the currently viewed sequence in the submission area of the tool
|
|
ready to perform a BLAST or Primer BLAST search. In addition protein records
|
|
have a link to pre-computed conserved domain results. These new links make it
|
|
easy to perform sequence analysis on the fly from any sequence record.</p></div><div id="JEKOtU220.Exhibits24_2"><h3>Exhibits</h3><p>NCBI will be exhibiting at the American Society for Microbiology’s
|
|
190<sup>th</sup> General Meeting on May 17-21 in Philadelphia,
|
|
Pennsylvania.</p></div></div><div id="JEKOtU220.Announce25_1"><h2 id="_JEKOtU220_Announce25_1_">Announce Lists and RSS Feeds</h2><p>Fifteen topic-specific mailing lists are described on the Announcement List summary
|
|
page. Announce lists provide email announcements about changes and updates to NCBI
|
|
resources. <a href="/Sitemap/Summary/email_lists.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html</a></p><p>Seven RSS feeds are now available from NCBI including news on PubMed, PubMed Central,
|
|
NCBI Bookshelf, LinkOut, HomoloGene, UniGene, and NCBI Announce. Please see:
|
|
<a href="/feed/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www.ncbi.nlm.nih.gov/feed/</a></p><p>Comments and questions about NCBI resources may be sent to NCBI at:
|
|
<a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@ofni" class="oemail">vog.hin.mln.ibcn@ofni</a>, or by calling 301-496-2475 between the
|
|
hours of 8:30 a.m. and 5:30 p.m. EST, Monday through Friday.</p></div><div id="may09rl1"><h2 id="_may09rl1_">References</h2><dl class="temp-labeled-list"><dl class="bkr_refwrap"><dt>1.</dt><dd><div class="bk_ref" id="JEKOtU220.Pap07">Papadopoulos J, Agarwala R. COBALT: constraint-based alignment tool for multiple protein
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sequences. <span class="ref-journal">COBALT: constraint-based alignment tool for multiple protein sequences.</span> 2007. [<a href="https://pubmed.ncbi.nlm.nih.gov/17332019" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 17332019</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>2.</dt><dd><div class="bk_ref" id="JEKOtU220.Kan96">Kaneko T. Cell biology of somatolactin. <span class="ref-journal">Cell biology of somatolactin.</span> 1996. pp. 1–24. [<a href="https://pubmed.ncbi.nlm.nih.gov/8843651" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 8843651</span></a>]</div></dd></dl></dl></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK6632_pubdet_">Publication Details</h2><h3>Author Information and Affiliations</h3><div class="contrib half_rhythm"><span itemprop="author">Peter Cooper</span>, PhD<div class="affiliation small">NCBI<div><span class="email-label">Email: </span><a href="mailto:dev@null" data-email="vog.hn.mln.ibcn@repooc" class="oemail">vog.hn.mln.ibcn@repooc</a></div></div></div><div class="contrib half_rhythm"><span itemprop="author">Dawn Lipshultz</span>, MS<div class="affiliation small">NCBI<div><span class="email-label">Email: </span><a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@tluhspil" class="oemail">vog.hin.mln.ibcn@tluhspil</a></div></div></div><h3>Publication History</h3><p class="small">Created: <span itemprop="datePublished">April 24, 2009</span>.</p><h3>Copyright</h3><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div></div><h3>Publisher</h3><p><a href="http://www.ncbi.nlm.nih.gov/news" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>, Bethesda (MD)</p><h3>NLM Citation</h3><p>Cooper P, Lipshultz D. NCBI News, May 2009. 2009 Apr 24. In: NCBI News [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 1991-2012. <span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/newsncbi/JFKPFT637.bid.1/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a></div><div class="small-screen-next"><a href="/books/n/newsncbi/apr09/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div></article><article data-type="fig" id="figobJEKOtU220may09fig1"><div id="JEKOtU220.may09fig1" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK6632/bin/may09image4.jpg" alt="Figure 1. COBALT interface and multiple alignments." /></div><h3><span class="label">Figure 1</span><span class="title">COBALT interface and multiple alignments</span></h3><div class="caption"><p>A. The basic COBALT interface
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with seven NCBI accessions from the Homologene cluster for ATP citrate
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lyase (Homologene ID 854) B. A portion of the COBALT multiple alignment
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showing the aberrant chimpanzee gene model, second line, <a href="/protein/332847769/?report=GenPept" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=genpept">XP_511495</a>. C.
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The sequences realigned after de-selecting the chimpanzee sequence. D.
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The multiple alignment without the chimpanzee sequence.</p></div></div></article><article data-type="fig" id="figobJEKOtU220may09fig2"><div id="JEKOtU220.may09fig2" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK6632/bin/may09image5.jpg" alt="Figure 2. BLAST, COBALT results, and phylogenetic tree of growth hormone family members for NCBI RefSeq proteins from teleost fishes." /></div><h3><span class="label">Figure 2</span><span class="title">BLAST, COBALT results, and phylogenetic tree of growth hormone family
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members for NCBI RefSeq proteins from teleost fishes</span></h3><div class="caption"><p>The sequences were
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collected by a BLAST search limited to NCBI known RefSeqs
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(refseq_protein database, srcdb_refseq_known Entrez limit) with bony
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fishes as an organism limit (top panel). The query sequence was the
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human prolactin precursor (<a href="/protein/4506105/?report=GenPept" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=genpept">NP_000939</a>). A multiple alignment was
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generated from the BLAST results. The phylogenetic tree shown (bottom
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panel) was based on a second COBALT alignment (middle panel) using only
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the fish sequences after de-selecting the human sequence on the original
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alignment and re-aligning. The tree shows three distinct subfamilies:
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growth hormone, prolactin, and the somatolactins, a group of pituitary
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hormones specific to fishes.</p></div></div></article></div><div id="jr-scripts"><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/libs.min.js"> </script><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.min.js"> </script></div></div>
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