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<i>Monday, January 27, 2014</i>
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</p><p>The Consensus Coding Sequence (CCDS) update for Homo sapiens annotation release 105 is now available on the <a href="https://www.ncbi.nlm.nih.gov/CCDS" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CCDS website</a> and <a href="ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">FTP site</a>. This release adds 349 new CCDS IDs to the human CCDS dataset and is based on comparative analysis of <a href="/books/n/newsncbi/N2013-08/?report=reader#news_08-27-2013-human-annotation-105">NCBI Homo sapiens annotation release 105</a> and <a href="http://useast.ensembl.org/Homo_sapiens/Info/Annotation#assembly" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Ensembl release 74</a>. The human CCDS dataset now includes 29,045 proteins that correspond to 18,683 genes.</p><p>This is the final CCDS update for human that is based on the human reference assembly GRCh37. The next CCDS update for human will be based on the updated assembly GRCh38 and is tentatively expected to be released in July 2014.</p></div><div id="news_01-21-2014-refseq-63-available"><h2 id="_news_01-21-2014-refseq-63-available_">RefSeq release 63 now available</h2><p>
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<i>Tuesday, January 21, 2014</i>
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</p><p>The <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">full RefSeq release 63</a> is now available with nearly 50 million records describing 37,371,278 proteins, 5,760,653 RNAs, and sequences from 33,485 different organisms.</p><p>Some important updates include the following:</p><p><b>Directory name change</b>: The RefSeq release directory “microbial” will be removed. Two new directories, “archaea” and “bacteria” will be added. This change will appear in release 65 in May 2014.</p><p><b>WGS process flow change</b>: WGS accessions will no longer be processed on a per-project (WGS prefix) basis. Instead, these accessions will be processed and packaged the same as non-WGS accessions. This will significantly reduce the number of files in the /complete/ and (new) /archaea/ and /bacteria/ directories. Therefore, there will no longer be a series of files named like “microbialNZ_*”. Instead, all WGS scaffolds will be found in concatenated files just like all other accession data. We will continue to provide a separate file for the WGS master records. This change will appear in release 65 in May 2014.</p><p><b>Human Genome GRCh38 Annotation plans</b>: The Genome Reference Consortium released an updated assembly for the human reference genome (GRCh38) in late December 2013. NCBI annotation of the RefSeq copy of this assembly is currently in progress. We anticipate releasing annotation in early to mid-February and including it in RefSeq release 64 in March 2014.</p><p>More details about RefSeq release 63 is included in the <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-statistics/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">release statistics</a> and <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">release notes</a>. In addition, reports indicating the accessions included <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/RefSeq-release63.catalog.gz" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">in the release</a> and <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release63.files.installed<ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release62.files.installed" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">the files installed</a> are available.</p></div><div id="news_01-21-2014-sequence-by-type"><h2 id="_news_01-21-2014-sequence-by-type_">Taxonomy database now shows type material, sequences from type specimens and strains now labeled in Entrez</h2><p>
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<i>Tuesday, January 21, 2014</i>
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</p><p>The naming, classification and identification of organisms traditionally relies on the concept of type material, which defines the representative examples ("name-bearing") of a species. For larger organisms, the type material is often a preserved specimen in a museum drawer, but the type concept also extends to type bacterial strains as cultures deposited in a culture collection. Of course, modern taxonomy also relies on molecular sequence information to define species.  In many cases, sequence information is available for type specimens and strains. Accordingly, the NCBI has started to curate type material from the Taxonomy database, and are using this data to label sequences from type specimens or strains in the sequence databases. The figure below shows type material as it appears in the NCBI taxonomy entry and a sequence record for the recently described African monkey species, <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1191211" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri"><i>Cercopithecus lomamiensis</i></a>.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="fignews01212014figure1typemateriali" co-legend-rid="figlgndnews01212014figure1typemateriali"><a href="/books/NBK431026/figure/news_01-21-2014.figure1typemateriali/?report=objectonly" target="object" title="Figure" class="img_link icnblk_img figpopup" rid-figpopup="fignews01212014figure1typemateriali" rid-ob="figobnews01212014figure1typemateriali"><img class="small-thumb" src="/books/NBK431026/bin/cms_cercopithecus.gif" src-large="/books/NBK431026/bin/cms_cercopithecus.jpg" alt="Figure 1" /></a><div class="icnblk_cntnt" id="figlgndnews01212014figure1typemateriali"><h4 id="news_01-21-2014.figure1typemateriali"><a href="/books/NBK431026/figure/news_01-21-2014.figure1typemateriali/?report=objectonly" target="object" rid-ob="figobnews01212014figure1typemateriali">Figure</a></h4><p class="float-caption no_bottom_margin"><i>Figure 1</i>. Type material information as it appears in the NCBI Taxonomy database (upper left) and nucleotide database (lower right) for <i>Cercopithecus lomamiensis</i>. Both records refer to the type material housed in the Yale Peabody Museum Mammalogy collection <a href="/books/NBK431026/figure/news_01-21-2014.figure1typemateriali/?report=objectonly" target="object" rid-ob="figobnews01212014figure1typemateriali">(more...)</a></p></div></div><p>Sequence from type material is particularly important because the species identification is virtually certain to be correct. The Entrez query <a href="https://www.ncbi.nlm.nih.gov/nuccore/?term=sequence+from+type%5Bfilter%5D" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">"sequence from type"[filter]</a> can be used to retrieve these sequence entries and can be used in combination with other queries as in the following examples.</p><p>
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<b>By Organism</b>
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</p><ul><li class="half_rhythm"><div>
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<a href="/nuccore/?term=sequence+from+type%5bfilter%5d+AND+bacteria%5borgn%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">sequence from type [filter] AND bacteria [Organism]</a>
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</div></li><li class="half_rhythm"><div>
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<a href="/nuccore/?term=sequence+from+type%5Bfilter%5D+AND+animals%5Borgn%5D" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">sequence from type [filter] AND animals [Organism]</a>
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</div></li></ul><p>
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<b>By Collection</b>
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</p><ul><li class="half_rhythm"><div><a href="/nuccore/?term=sequence+from+type%5bfilter%5d+AND+collection+cbs%5bprop%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">"sequence from type"[filter] AND collection cbs</a> (type strains at the CBS culture collection)</div></li><li class="half_rhythm"><div><a href="/nuccore/?term=sequence+from+type%5bfilter%5d+AND+collection+mcz%5bprop%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">"sequence from type"[filter] AND collection mcz</a> (type specimen at the Museum of Comparative Zoology)</div></li></ul><p>
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<b>By Author</b>
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</p><ul><li class="half_rhythm"><div>
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<a href="/nuccore/?term=sequence+from+type%5bfilter%5d+AND+hedges+sb%5bau%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">"sequence from type"[filter] AND hedges sb</a>
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</div></li><li class="half_rhythm"><div>
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<a href="/nuccore/?term=sequence+from+type%5bfilter%5d+AND+baldwin+c%5bau%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">"sequence from type"[filter] AND Baldwin c</a>
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</div></li></ul><p>As shown in the figure below, “sequence from type”[filter] is also useful as an Entrez query to limit BLAST searches to reliably identified sequences, particularly when working with prokaryotes.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="fignews01212014figure2thechoosesear" co-legend-rid="figlgndnews01212014figure2thechoosesear"><a href="/books/NBK431026/figure/news_01-21-2014.figure2thechoosesear/?report=objectonly" target="object" title="Figure" class="img_link icnblk_img figpopup" rid-figpopup="fignews01212014figure2thechoosesear" rid-ob="figobnews01212014figure2thechoosesear"><img class="small-thumb" src="/books/NBK431026/bin/cms_sequence-from-type-filter-in-blast.gif" src-large="/books/NBK431026/bin/cms_sequence-from-type-filter-in-blast.jpg" alt="Figure 2" /></a><div class="icnblk_cntnt" id="figlgndnews01212014figure2thechoosesear"><h4 id="news_01-21-2014.figure2thechoosesear"><a href="/books/NBK431026/figure/news_01-21-2014.figure2thechoosesear/?report=objectonly" target="object" rid-ob="figobnews01212014figure2thechoosesear">Figure</a></h4><p class="float-caption no_bottom_margin"><i>Figure 2</i>. The “Choose Search Set” section of the Microbial Genomes BLAST page. The optional Organism limit, enterobacteria,  and the Entrez query ‘Sequence from type[Filter]’ restricts the search to sequences from <a href="/books/NBK431026/figure/news_01-21-2014.figure2thechoosesear/?report=objectonly" target="object" rid-ob="figobnews01212014figure2thechoosesear">(more...)</a></p></div></div><p>Stay tuned for more developments and added features coming to the Taxonomy database.</p></div><div id="news_01-16-2014-remap-transitions-data-to-grch38"><h2 id="_news_01-16-2014-remap-transitions-data-to-grch38_">New NCBI Insights blog: NCBI Remap tool helps you transition to newest human reference genome assembly, GRCh38</h2><p>
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<i>Thursday, January 16, 2014</i>
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</p><p><a href="https://www.ncbi.nlm.nih.gov/genome/tools/remap" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI’s Genome Remapping Service (NCBI Remap)</a> allows you to map annotation data from one genomic assembly to another for a selected set of organisms. This may be particularly helpful in updating your annotations for the human reference genome assembly, which has recently been updated to the new version, <a href="http://ncbiinsights.ncbi.nlm.nih.gov/2013/12/24/introducing-the-new-human-genome-assembly-grch38/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GRCh38</a>. The <a href="http://ncbiinsights.ncbi.nlm.nih.gov/2014/01/16/ncbis-genome-remapping-service-assists-in-the-transition-to-the-new-human-genome-reference-assembly-grch38/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">newest blog post on NCBI Insights</a> describes how Remap works and how it allows you to analyze data in the context of the newest genome assembly. Finally, the blog post provides links to Remap-related documentation including an overview, FAQs, and a YouTube tutorial.</p></div><div id="news_01-14-2014-sviewer-pdf-youtube-video"><h2 id="_news_01-14-2014-sviewer-pdf-youtube-video_">Sequence Viewer PDF rendering available - YouTube video tutorial</h2><p>
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<i>Tuesday, January 14, 2014</i>
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</p><p>NCBI has created a YouTube <a href="http://www.youtube.com/watch?v=oym8dPB0BSE" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">video tutorial</a> showing you how to generate a PDF rendering of your Sequence Viewer display. The short clip takes you through the downloading process, and shows you what you can do with your file after creating a PDF.</p></div><div id="news_01-14-2014-genome-workbench-updated"><h2 id="_news_01-14-2014-genome-workbench-updated_">Genome Workbench Update 2.7.12</h2><p>
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<i>Tuesday, January 14, 2014</i>
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</p><p>Genome Workbench 2.7.12 has been released. The update includes several new features like a faster Tree Renderer, redesigned data import and an improved GFF format reader. The <a href="https://www.ncbi.nlm.nih.gov/tools/gbench/releasenotes/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">release notes</a> include more information on features, fixes and improvements.</p></div><div id="news_01-09-2014-new-vastplus-released"><h2 id="_news_01-09-2014-new-vastplus-released_">VAST+ released: Find similar 3D structures for macromolecular complexes</h2><p>
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<i>Thursday, January 09, 2014</i>
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</p><p><a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">VAST+</a> is a new tool designed to identify macromolecules that have similar 3-dimensional structures with an emphasis on finding similar macromolecular complexes. The similarities are calculated using purely geometric criteria without regard to sequence similarity, and therefore can identify distant homologs.</p><p>This new tool is built upon the original <a href="https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Vector Alignment Search Tool (VAST)</a> and expands the capabilities of that program by taking into account the <a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/docs/vastplus_help.html#OutputBiologicalUnit" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">biological unit</a> ("biounit") of each structure, not just individual protein chains or their substructures.</p><p>A recent <a href="https://www.ncbi.nlm.nih.gov/pubmed/24319143" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">publication </a>provides detailed information about the VAST+ algorithm. In addition, the extensive VAST+ help document includes a <a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/docs/vastplus_help.html#Compare" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">comparison of original VAST and VAST+</a>, as well as <a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/docs/vastplus_help.html#DatabaseApplications" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">examples of how can this tool can be used</a> to learn more about proteins.</p><p>
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<i>Please note that in order to view the 3D superpositions of similar biological units, you must install the most recent version of the NCBI molecular viewing software, <a href="https://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Cn3D 4.3.1</a>.</i>
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</p><p>
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<a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=1B26" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">
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<div class="graphic"><img src="/books/NBK431026/bin/cms_VASTplus_Example.jpg" alt="Vastplus Example of 1B26" /></div>
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</a>
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</p><p>Figure. <a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=1B26" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">VAST+ search results</a> for <i>Thermotoga maritima</i> Glutamate Dehydrogenase (PDB ID <a href="https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=11869" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">1B26</a>) with detailed view of a match to <a href="https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=5314" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">1GTM</a>.</p><div id="news_01-09-2014.formoreinformation"><h3>
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For more information:</h3><ul><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">VAST+ home page</a>
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</div></li><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/pubmed/24319143" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Publication in Nucleic Acids Research</a>
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</div></li><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/docs/vastplus_help.html#DatabaseApplications" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Vast+ examples</a>
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</div></li><li class="half_rhythm"><div>
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<a href="https://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Cn3D home page</a>
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</div></li></ul></div></div><div id="news_1-8-2014-librarians-guide-to-ncbi-april-2014"><h2 id="_news_1-8-2014-librarians-guide-to-ncbi-april-2014_">NCBI Insights blog: A Librarian's Guide to NCBI - an intensive training course for medical librarians to be offered April 2014</h2><p>
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<i>Wednesday, January 08, 2014</i>
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</p><p>The NCBI in partnership with the <a href="http://nnlm.gov/ntc/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">National Library of Medicine Training Center</a> (NTC) will offer the Librarian’s Guide to NCBI course on the NIH campus in April 2014. This will be the second presentation of the course; it was previously offered in the spring of 2013 (NCBI Insights <a href="http://ncbiinsights.ncbi.nlm.nih.gov/2013/04/11/a-librarians-guide-to-ncbi-a-new-education-initiative/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">April 11</a> and <a href="http://ncbiinsights.ncbi.nlm.nih.gov/2013/05/06/a-librarians-guide-to-ncbi-course-follow-up/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">May 6</a>, 2013). After the course, we will post lecture slides and hands-on practical exercises on the education area of the NCBI FTP site and video tutorials of the course lectures will be available on the NCBI YouTube channel. <a href="ftp://ftp.ncbi.nlm.nih.gov/pub/education/librarian_guide/2013/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Materials</a> from the 2013 course are available, as well as lecture videos for the <a href="http://www.youtube.com/watch?v=-uBY0rnkf8U" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">expression module</a>. More information, including prerequisites, is available in the <a href="http://ncbiinsights.ncbi.nlm.nih.gov/2014/01/08/a-librarians-guide-to-ncbi-an-intensive-training-course-for-medical-librarians-to-be-offered-april-2014/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">newest NCBI Insights blog post</a>.</p></div><div id="news_1-8-2014-mouse-genome-annotation-release-104"><h2 id="_news_1-8-2014-mouse-genome-annotation-release-104_">Mouse genome annotation release 104 available</h2><p>
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<i>Wednesday, January 08, 2014</i>
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</p><p>The mouse (<i>Mus musculus</i>) genome annotation has recently been updated to <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Mus_musculus/104" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">annotation release 104</a> and is now available in the Nucleotide, Protein sequence and Gene databases, is searchable using <a href="https://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=10090" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">BLAST</a>, and can be downloaded from the <a href="ftp://ftp.ncbi.nih.gov/genomes/Mus_musculus" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">FTP site</a>.</p><p>Mouse annotation release 104, based on the sequence assemblies GRCm38.p2 (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.22" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GCF_000001635.22</a>) and Mm_Celera (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000002165.2" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GCF_000002165.2</a>), identifies a total of 35,389 genes, as well as 100,581 transcripts on GRCm38.p2. RNA-Seq data from 31 distinct BioSample accessions were aligned to assist in gene prediction. More statistics are available in the <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Mus_musculus/104" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">annotation report</a>.</p><p>See what other annotation runs are in progress on the <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/status/#inprogress" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Eukaryotic Genome Annotation Pipeline status page</a>.</p></div><div id="news_1-7-2014-blast-2-2-29"><h2 id="_news_1-7-2014-blast-2-2-29_">BLAST+ 2.2.29 now available</h2><p>
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<i>Tuesday, January 07, 2014</i>
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</p><p>Stand-alone BLAST version 2.2.29+ is now available for download from the <a href="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">FTP site</a>. BLAST 2.2.29+ provides a number of important improvements and bug fixes. Some improvements include improved blastn batch query performance, source releases build optimized multi-thread binaries by default, and improved multithreading by better dividing the BLAST database among threads. The <a href="/books/NBK131777/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">BLAST Release notes</a> lists more upgrades and fixes.</p></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK431026_pubdet_">Publication Details</h2><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>NCBI News [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 1991-2012. NCBI News, January 2014.<span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/newsncbi/N2014-02/?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/N2013-12/?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="figobnews01212014figure1typemateriali"><div id="news_01-21-2014.figure1typemateriali" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK431026/bin/cms_cercopithecus.jpg" alt="cercopithecus" /></div><div class="caption"><p><b>Figure 1</b>. Type material information as it appears in the NCBI Taxonomy database (upper left) and nucleotide database (lower right) for <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1191211" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri"><i>Cercopithecus lomamiensis</i></a>. Both records refer to the type material housed in the Yale Peabody Museum Mammalogy collection (lower left, <a href="http://peabody.research.yale.edu/cgi-bin/Query.Ledger?LE=mam&SU=0&ID=14080" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">YPM MAM 140180</a>).</p></div></div></article><article data-type="fig" id="figobnews01212014figure2thechoosesear"><div id="news_01-21-2014.figure2thechoosesear" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK431026/bin/cms_sequence-from-type-filter-in-blast.jpg" alt="sequence from type filter in blast" /></div><div class="caption"><p><b>Figure 2</b>. The “Choose Search Set” section of the <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Microbial Genomes BLAST page</a>. The optional Organism limit, enterobacteria,  and the Entrez query ‘Sequence from type[Filter]’ restricts the search to sequences from enterobacteria type strains.</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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<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"> </script>
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</html>
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