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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>NCBI News [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 1991-2012. </p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/newsncbi/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-newsncbi-lrg.png" alt="Cover of NCBI News" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>NCBI News [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK6632_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK6632_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/news" ref="pagearea=page-banner&amp;targetsite=external&amp;targetcat=link&amp;targettype=publisher">National Center for Biotechnology Information (US)</a>; 1991-2012.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/newsncbi/">Index of Issues</a></li></ul></div><div class="bk_noprnt"><form method="get" action="/books/n/newsncbi/" id="bk_srch"><div class="bk_search"><label for="bk_term" class="offscreen_noflow">Search term</label><input type="text" title="Search this book" id="bk_term" name="term" value="" data-jig="ncbiclearbutton" /> <input type="submit" class="jig-ncbibutton" value="Search this book" submit="false" style="padding: 0.1em 0.4em;" /></div></form></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/newsncbi/JFKPFT637.bid.1/" title="Previous page in this title">&lt; Prev</a><a class="active page_link next" href="/books/n/newsncbi/apr09/" title="Next page in this title">Next &gt;</a></div></div></div></div></div>
<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK6632_"><span class="title" itemprop="name">NCBI News, May 2009</span></h1><p class="contrib-group"><span itemprop="author">Peter Cooper</span>, PhD and <span itemprop="author">Dawn Lipshultz</span>, MS.</p><a data-jig="ncbitoggler" href="#__NBK6632_ai__" style="border:0;text-decoration:none">Author Information and Affiliations</a><div style="display:none" class="ui-widget" id="__NBK6632_ai__"><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></div><p class="small">Created: <span itemprop="datePublished">April 24, 2009</span>.</p><p><em>Estimated reading time: 8 minutes</em></p></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
outbreak and is making every effort to make the sequences available as soon as
possible. You can access the recent flu sequences and retrieve them individually
from a special influenza virus resource page that is updated daily:</p><p>
<a href="/genomes/FLU/SwineFlu.html" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html</a>
</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&amp;targetsite=external&amp;targetcat=link&amp;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 &#x0201c;show&#x0201d; line of the form, set the species
to &#x0201c;Influenzavirus A&#x0201d;, the host to
&#x0201c;human&#x0201d;, the Country/Region to
&#x0201c;any&#x0201d;, the collection date range to
&#x0201c;2009/04:2009/05&#x0201d;, and the subtype to
&#x0201c;H1N1&#x0201d;. Set the viral segment to
&#x0201c;any&#x0201d; to get all segments, or select a specific segment
or protein if desired. Click the &#x0201c;Get sequences&#x0201d; 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
&#x02013; protein, coding region, nucleotide &#x02013; from the
&#x0201c;Select FASTA sequence for download&#x0201d; 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 &#x0201c;Select accession list to download&#x0201d; 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&amp;targetsite=external&amp;targetcat=link&amp;targettype=uri">www.ncbi.nlm.nih.gov/sites/batchentrez</a>
</p><p>Click the &#x0201c;Browse&#x0201d; button at the top of the batch Entrez
page and point to the file containing the downloaded list of accessions. Click
the &#x0201c;Retrieve&#x0201d; 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&amp;targetsite=external&amp;targetcat=link&amp;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 &#x0201c;Display&#x0201d; 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 &#x0201c;Send
to&#x0201d; 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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=entrez&amp;targetcat=term&amp;targettype=nuccore">FJ966079-FJ966086</a>
available in the Entrez nucleotide service.</p><p>
<a href="/sites/entrez?db=nuccore" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=entrez&amp;targetcat=term&amp;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="bk_pop" href="#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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=entrez&amp;targetcat=link&amp;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 &#x0201c;Multiple Alignment&#x0201d; link in the
&#x0201c;Other reports&#x0201d; 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&amp;targetsite=entrez&amp;targetcat=link&amp;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 &#x0201c;Algorithm
parameters&#x0201d; of the BLAST form. A COBALT alignment can be generated
by clicking the &#x0201c;Multiple alignment&#x0201d; link in the
&#x0201c;Other reports&#x0201d; 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 &#x0201c;Phylogenetic tree&#x0201d; 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&#x00026;part=newsarchive" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;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="bk_pop" href="#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 &#x0201c;Recent Results&#x0201d; 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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&#x02019;s SRA database. To perform a search, go to <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&#x00026;PROGRAM=blastn&#x00026;BLAST_PROGRAMS=megaBlast&#x00026;PAGE_TYPE=BlastSearch&#x00026;BLAST_SPEC=SRA" ref="pagearea=body&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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&#x02019;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&amp;targetsite=external&amp;targetcat=link&amp;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&amp;targetsite=external&amp;targetcat=link&amp;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"><dt>1.</dt><dd><div class="bk_ref" id="JEKOtU220.Pap07">Papadopoulos J, Agarwala R. COBALT: constraint-based alignment tool for multiple protein
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&amp;targetsite=entrez&amp;targetcat=link&amp;targettype=pubmed">PubMed<span class="bk_prnt">: 17332019</span></a>]</div></dd><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. 124. [<a href="https://pubmed.ncbi.nlm.nih.gov/8843651" ref="pagearea=cite-ref&amp;targetsite=entrez&amp;targetcat=link&amp;targettype=pubmed">PubMed<span class="bk_prnt">: 8843651</span></a>]</div></dd></dl></div><div id="bk_toc_contnr"></div></div></div>
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