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<script type="text/javascript" src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.boots.min.js"> </script><title>NCBI News, December 2016 - NCBI News - NCBI Bookshelf</title>
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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="_NBK431038_"><span class="title" itemprop="name">NCBI News, December 2016</span></h1><p class="fm-aai"><a href="#_NBK431038_pubdet_">Publication Details</a></p><p><em>Estimated reading time: 4 minutes</em></p></div></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="news_12-23-2016-sviewer-discrepancies-youtube"><h2 id="_news_12-23-2016-sviewer-discrepancies-youtube_">New YouTube video: Sequence Viewer: Display Translation Discrepancies</h2><p>
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<i>Friday, December 23, 2016</i>
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</p><p>The <a href="https://www.youtube.com/watch?v=x5eZfJtkME4" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">newest video</a> on the <a href="https://www.youtube.com/user/NCBINLM" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI YouTube channel</a> is a brief introduction to a new set of sequence viewer renderings that better display discrepancies between genomic sequence and annotated features. These discrepancies can occur because RefSeq gene models based on the current genomic sequence can differ from RefSeq transcripts and corresponding proteins that come from our continuous curation efforts. For links to examples used in the video, see the Sequence Viewer <a href="https://www.ncbi.nlm.nih.gov/tools/sviewer/translationdiscrepancies" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">tutorial</a>.</p><p>Subscribe to the <a href="https://www.youtube.com/user/NCBINLM" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI YouTube channel</a> to receive alerts about new videos ranging from quick tips to full webinar presentations.</p><p>Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the <a href="https://www.ncbi.nlm.nih.gov/nucleotide/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Nucleotide</a> and <a href="https://www.ncbi.nlm.nih.gov/guide/proteins/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Protein</a> databases.</p><p>
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<div class="graphic"><img src="/books/NBK431038/bin/cms_sequence-viewer-fb-pic.jpg" alt="Sequence Viewer sample" /></div>
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</p></div><div id="news_12-23-2016-ncbi-insights-bulk-converting-gis"><h2 id="_news_12-23-2016-ncbi-insights-bulk-converting-gis_">New NCBI Insights post: Converting Lots of GI Numbers to Accession.version</h2><p>
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<i>Friday, December 23, 2016</i>
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</p><p>The <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2016/12/23/converting-lots-of-gi-numbers-to-accession-version/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">latest post</a> on the NCBI Insights blog provides a bulk conversion resource for those who those who need to convert more than a few thousand GI numbers to accession.version identifiers.</p><p>As you may already know, accession.version identifiers, rather than GI numbers, will be the <a href="/books/n/newsncbi/N2016-03/?report=reader#news_03-02-2016-phase-out-of-GI-numbers">primary identifiers for sequence records at NCBI</a>.</p><p><a href="http://ncbiinsights.ncbi.nlm.nih.gov/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI Insights</a> is the official NCBI blog, where we share science feature stories, quick tips and what’s new at NCBI.</p></div><div id="news_12-22-2016-ccds-mouse-21"><h2 id="_news_12-22-2016-ccds-mouse-21_">CCDS release 21 for mouse is public in Gene</h2><p>
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<i>Thursday, December 22, 2016</i>
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</p><p>The <a href="https://www.ncbi.nlm.nih.gov/CCDS/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Consensus Coding Sequence (CCDS)</a> update that compares NCBI's <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Mus_musculus/106/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Mus musculus annotation release 106</a> to Ensembl's release 86 is now available in <a href="https://www.ncbi.nlm.nih.gov/gene/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Gene</a>. This update adds 938 new CCDS IDs, and adds 137 genes into the mouse CCDS set. CCDS release 21 includes a total of 25,757 CCDS IDs that correspond to 20,354 GeneIDs.</p><p>Also, note that the <a href="https://www.ncbi.nlm.nih.gov/projects/CCDS/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CCDS survey</a> is still open. NCBI and the CCDS collaboration invite you to take a survey that will help us assess how the human and mouse Consensus CDS data is being accessed and used by the scientific community. We welcome your feedback and suggestions on this data collection. Data gathered from the survey will help us plan the future direction of the CCDS project.</p></div><div id="news_12-15-2016-ncbi-minute-bulk-converting-gis"><h2 id="_news_12-15-2016-ncbi-minute-bulk-converting-gis_">December 21st NCBI Minute: Bulk Conversion of NCBI Sequence GI Identifiers to accession.version</h2><p>
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<i>Thursday, December 15, 2016</i>
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</p><p>Next Wednesday, NCBI will demonstrate how to use a downloadable database and Python script to convert GI identifiers to accession.version. The file and service that will be used are suitable for one-time conversion of very large sets of data.</p><p><b>Date and time:</b> Wednesday, December 21, 2016 12:00 PM - 12:15 PM EST</p><p><b>Registration URL:</b>
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<a href="https://attendee.gotowebinar.com/register/6267508028097746946" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://attendee.gotowebinar.com/register/6267508028097746946</a></p><p>After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the <a href="https://www.youtube.com/user/NCBINLM" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI YouTube channel</a>. Any related materials will be accessible on the <a href="https://www.ncbi.nlm.nih.gov/home/coursesandwebinars.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Webinars and Courses page</a>; you can also learn about future webinars on this page.</p></div><div id="news_12-12-2016-variant-data-clinvar"><h2 id="_news_12-12-2016-variant-data-clinvar_">Variant interpretations from Illumina double ClinVar data</h2><p>
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<i>Monday, December 12, 2016</i>
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</p><p>On Dec 7, 2016, ClinVar released <a href="https://www.ncbi.nlm.nih.gov/clinvar/submitters/504895" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">138,334 variant interpretations</a> submitted by Illumina Clinical Services Laboratory (ICSL) in San Diego, CA. This dataset represents a 57% increase in the number of submitted interpretations and makes ICSL the largest source of data in ClinVar. The contribution from ICSL also provides 78,590 novel variants to the database, an increase of 45% over the previous total of 173,782 variants.</p><p>The data were generated from clinical whole genome sequencing performed in the ICSL; variants were interpreted when the associated gene was in a predefined list of genes associated with Mendelian disorders or when the gene-disease relationship had been manually curated. Information about the criteria that ICSL uses to interpret variants is available on the <a href="https://submit.ncbi.nlm.nih.gov/ft/byid/4jQgNGYk/ICSL_Variant_Classification_20161018.pdf" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI website</a>.</p><p>ICSL has shared data through other NCBI resources as well, including the <a href="https://www.ncbi.nlm.nih.gov/gtr/labs/504895/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Genetic Testing Registry</a> and the <a href="https://www.ncbi.nlm.nih.gov/variation/tools/get-rm/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GeT-RM browser</a>.</p><p><a href="https://www.ncbi.nlm.nih.gov/clinvar" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">ClinVar</a> is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. Interpretations of variants are submitted to ClinVar by clinical testing laboratories, research laboratories, locus-specific databases, genetics clinics, expert panels, and professional societies that establish practice guidelines. The database currently holds 374,018 submitted interpretations representing 263,220 variants. ClinVar provides a public forum for variant interpretations and evidence, so that interpretations may be shared and subjected to peer review.</p></div><div id="news_12-12-2016-human-genome-resource-page"><h2 id="_news_12-12-2016-human-genome-resource-page_">The new Human Genome Resources site: a portal for exploration of the human genome</h2><p>
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<i>Monday, December 12, 2016</i>
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</p><p>The new <a href="https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Human Genome Resources site</a> offers access to visualization and analysis tools available for the human genome, as well as other relevant tools like <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__9606__9558" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">BLAST</a>, the <a href="https://www.ncbi.nlm.nih.gov/genome/tools/remap" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI remapping service</a> and databases that provide human molecular data. The resources are sorted into categories like Find, View, Download and Learn, making it easier to find what you need.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="fignews12122016figure1thenewncbihum" co-legend-rid="figlgndnews12122016figure1thenewncbihum"><a href="/books/NBK431038/figure/news_12-12-2016.figure1thenewncbihum/?report=objectonly" target="object" title="Figure" class="img_link icnblk_img figpopup" rid-figpopup="fignews12122016figure1thenewncbihum" rid-ob="figobnews12122016figure1thenewncbihum"><img class="small-thumb" src="/books/NBK431038/bin/cms_human-genome-resources-page.gif" src-large="/books/NBK431038/bin/cms_human-genome-resources-page.jpg" alt="Figure 1" /></a><div class="icnblk_cntnt" id="figlgndnews12122016figure1thenewncbihum"><h4 id="news_12-12-2016.figure1thenewncbihum"><a href="/books/NBK431038/figure/news_12-12-2016.figure1thenewncbihum/?report=objectonly" target="object" rid-ob="figobnews12122016figure1thenewncbihum">Figure</a></h4><p class="float-caption no_bottom_margin"><i>Figure 1.</i> The new NCBI Human Genome Resources webpage. </p></div></div><p>Some specific goals that you can accomplish through the site's guidance are:</p><ul><li class="half_rhythm"><div>Finding information on individual genes that <a href="https://www.ncbi.nlm.nih.gov/refseq/about/human/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI RefSeq staff annotate on the human genome assemblies</a> and are archived in the <a href="https://www.ncbi.nlm.nih.gov/gene" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Gene database</a>.</div></li><li class="half_rhythm"><div>Visualizing and analyzing the genome by accessing individual chromosomes in the <a href="https://www.ncbi.nlm.nih.gov/genome/gdv/?context=gene&acc=4318" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Genome Data Viewer</a> and other available viewers.</div></li><li class="half_rhythm"><div>Comparing your sequences with the sequences of the <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__9606__9558" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">human genome assemblies (BLAST)</a>.</div></li><li class="half_rhythm"><div>Navigating to the clinical and variation data through the complete listing of NCBI's clinical and variation resources.</div></li><li class="half_rhythm"><div>Accessing details about the human genome assemblies and annotation.</div></li><li class="half_rhythm"><div>Accessing various large datasets for download on the NCBI FTP site.</div></li><li class="half_rhythm"><div>Remapping annotation data between different assemblies (<a href="https://www.ncbi.nlm.nih.gov/genome/tools/remap" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI Genome Remapping Service</a>).</div></li></ul><p>In addition, the portal includes an extensive listing of learning resources that may help you have a better understanding of the wealth of information associated with the human genome.</p></div><div id="news_12-08-2016-sequence-viewer-318"><h2 id="_news_12-08-2016-sequence-viewer-318_">Sequence Viewer 3.18 is now available</h2><p>
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<i>Thursday, December 08, 2016</i>
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</p><p><a href="https://www.ncbi.nlm.nih.gov/tools/sviewer/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Sequence Viewer 3.18</a> has several new features, improvements and bug fixes, including improved handling of <a href="https://www.ncbi.nlm.nih.gov/tools/sviewer/translationdiscrepancies/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">translation discrepancies</a>, a new option for <a href="https://www.ncbi.nlm.nih.gov/tools/sviewer/embedding-api/#bookmark15" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">"Left-to-right translations"</a> for the six frame translation track, and improved code generation. For a full list of changes, see the Sequence Viewer <a href="https://www.ncbi.nlm.nih.gov/tools/sviewer/release-notes/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">release notes</a>.</p><p>Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the <a href="https://www.ncbi.nlm.nih.gov/nucleotide/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Nucleotide</a> and <a href="https://www.ncbi.nlm.nih.gov/guide/proteins/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Protein</a> databases.</p></div><div id="news_12-06-2016-ncbi-insights-convert-gi-accver"><h2 id="_news_12-06-2016-ncbi-insights-convert-gi-accver_">New on NCBI Insights: Converting GI Numbers to Accession.version</h2><p>
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<i>Tuesday, December 06, 2016</i>
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</p><p>The latest blog post on <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2016/12/06/converting-gi-numbers-to-accession-version/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI Insights</a> shows users how to convert GI numbers to accession.version with EFetch.</p><p><a href="https://ncbiinsights.ncbi.nlm.nih.gov/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI Insights</a> is the official NCBI blog, where we share science feature stories, quick tips and what's new at NCBI.</p></div><div id="news_12-02-2016-ncbi-ascb2016"><h2 id="_news_12-02-2016-ncbi-ascb2016_">NCBI Tech Talk and Booth at the American Society for Cell Biology 2016 National Meeting</h2><p>
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<i>Friday, December 02, 2016</i>
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</p><p>NCBI staff will be participating in the <a href="http://www.ascb.org/2016meeting/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">ASCB 2016 National Meeting</a> from Sunday, December 4 to Tuesday, December 6. We will be at booth #939 from 9AM -4PM PDT Sunday to Tuesday, and will present a Tech Talk on Sunday, December 4 at 5:30PM PDT in Theater 2.</p><p>The Tech Talk, "Five Useful Teaching Examples Using NCBI BLAST", will present demonstrations that highlight features of BLAST. These readily adaptable examples are useful for teaching biology principles and techniques including evolution, gene expression analysis and more.</p></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK431038_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, December 2016.<span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/newsncbi/N2017-01/?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/N2016-11/?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="figobnews12122016figure1thenewncbihum"><div id="news_12-12-2016.figure1thenewncbihum" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK431038/bin/cms_human-genome-resources-page.jpg" alt="human genome resources page" /></div><div class="caption"><p><b>Figure 1.</b> The new NCBI Human Genome Resources webpage.</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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