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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="_NBK431035_"><span class="title" itemprop="name">NCBI News, August 2016</span></h1><p class="fm-aai"><a href="#_NBK431035_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_08-30-2016-genomes-ftp-reorganization"><h2 id="_news_08-30-2016-genomes-ftp-reorganization_">Genomes FTP site data organization to change on September 20, 2016</h2><p>
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<i>Tuesday, August 30, 2016</i>
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</p><p>NCBI is moving the contents of the "all" and "ASSEMBLY_REPORTS/All" directories on the <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Genomes FTP site</a>. Currently, listing the contents of these two directories is impractical because they contain many thousands of directories or files.</p><div id="news_08-30-2016.reorganizationofftpf"><h3>
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Reorganization of ftp://ftp.ncbi.nlm.nih.gov/genomes/all</h3><p>The genome assembly directories currently directly under "all" will be moved into a new 4-level structure under genomes/all.</p><p>Two new directories under "all" will be named for the accession prefix (GCA or GCF). These directories will contain another three levels of directories named for digits 1-3, 4-6 & 7-9 of the assembly accession, creating paths like <i>genomes/all/GCA/xxx/xxx/xxx/</i> and <i>genomes/all/GCF/xxx/xxx/xxx/</i>. For example:</p><ul><li class="half_rhythm"><div>The data currently in genomes/all/GCA_000001405.23_GRCh38.p8 will be moved to genomes/all/GCA/000/001/405/GCA_000001405.23_GRCh38.p8.</div></li><li class="half_rhythm"><div>The data currently in genomes/all/GCF_001696305.1_UCN72.1 will be moved to genomes/all/GCF/001/696/305/GCF_001696305.1_UCN72.1.</div></li></ul><div id="news_08-30-2016.scheduleofchanges"><h4>
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Schedule of changes</h4><p>On September 20, 2016:</p><ul><li class="half_rhythm"><div>New directories genomes/all/GCA, genomes/all/GCF and the three levels of directories named for groups of digits in the assembly accession will be added.</div></li><li class="half_rhythm"><div>Individual genome assembly data directories directly under genomes/all will be moved into the new directory structure under genomes/all/GCA & GCF.</div></li><li class="half_rhythm"><div>Assembly data directories directly under genomes/all will be replaced by symbolic links to the corresponding directory in the new structure.</div></li><li class="half_rhythm"><div>The old and new data organizations will be maintained in parallel for 6 weeks.</div></li></ul><p>On December 1, 2016:</p><ul><li class="half_rhythm"><div>The old paths to individual genome assembly data directories directly under genomes/all will be removed.</div></li><li class="half_rhythm"><div>All access to genome assembly data under genomes/all/ will need to use the genomes/all/GCA/xxx/xxx/xxx/ & genomes/all/GCF/xxx/xxx/xxx/ paths.</div></li></ul></div><div id="news_08-30-2016.impact1"><h4>
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Impact</h4><p>Users who access genome assembly data by any of the following methods will not be affected by this change:</p><ul><li class="half_rhythm"><div>Following a link to "Download the GenBank assembly" or "Download the RefSeq assembly" from an Assembly details page</div></li><li class="half_rhythm"><div>Navigating the genomes/genbank or genomes/refseq paths of the genomes FTP site</div></li><li class="half_rhythm"><div>Using the ftp_path provided in the assembly_summary.txt files provided on the genomes FTP site</div></li></ul><p>Users who mirror all data under genomes/all will get two copies of the data for each genome assembly during the transition period, unless they modify their scripts to only take data from genomes/all/GCA & GCF.</p><p>Other changes:</p><ul><li class="half_rhythm"><div>Scripts that retrieve data using hard-coded paths to individual genome assembly directories directly under genomes/all will fail after the transition period</div></li><li class="half_rhythm"><div>Links from non-NCBI web pages to individual genome assembly directories directly under genomes/all will fail after the transition period</div></li><li class="half_rhythm"><div>Published paths to individual genome assembly directories directly under genomes/all will fail after the transition period</div></li></ul></div></div><div id="news_08-30-2016.removalofftpftpncbin"><h3>
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Removal of ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All</h3><p>First, the assembly reports currently under genomes/ASSEMBLY_REPORTS/All will be moved into the assembly data directories in the new directory hierarchy under genomes/all/GCA & genomes/all/GCF described above, replacing the symbolic links to the assembly report files that currently exist in this location. The assembly report files in the assembly data directories will retain the name previously provided by the symbolic link.</p><ul><li class="half_rhythm"><div>{assembly_accession.version}.assembly.txt will appear as {assembly_accession.version}_{assembly_name}_assembly_report.txt</div></li><li class="half_rhythm"><div>{assembly_accession.version}.stats.txt will appear as {assembly_accession.version}_{assembly_name}_assembly_stats.txt</div></li><li class="half_rhythm"><div>{assembly_accession.version}.regions.txt will appear as {assembly_accession.version}_{assembly_name}_assembly_regions.txt</div></li></ul><p>Then, the genomes/ASSEMBLY_REPORTS/All directory will be removed.</p><div id="news_08-30-2016.schedule"><h4>
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Schedule</h4><p>On September 20, 2016:</p><ul><li class="half_rhythm"><div>The assembly reports currently under genomes/ASSEMBLY_REPORTS/All will be moved into the assembly data directories, replacing the symbolic links currently in the data directories.</div></li><li class="half_rhythm"><div>The assembly reports under genomes/ASSEMBLY_REPORTS/All will be replaced by symbolic links to the corresponding report in the assembly data directory.</div></li><li class="half_rhythm"><div>The old and new data organizations for assembly reports will be maintained in parallel for 6 weeks.</div></li></ul><p>On December 1, 2016:</p><ul><li class="half_rhythm"><div>The old paths to assembly reports under genomes/ASSEMBLY_REPORTS/All will be removed.</div></li><li class="half_rhythm"><div>The genomes/ASSEMBLY_REPORTS/All directory will be removed.</div></li><li class="half_rhythm"><div>All access to assembly reports will need to use the genomes/all/GCA/, genomes/all/GCF, genomes/genbank or genomes/refseq paths to the individual assembly data directories.</div></li></ul></div><div id="news_08-30-2016.impact2"><h4>
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Impact</h4><p>Users who access assembly reports by any of the following methods will not be affected by this change:</p><ul><li class="half_rhythm"><div>Following a link to "Download the full sequence report" from an Assembly details page</div></li><li class="half_rhythm"><div>From an assembly data directory under the genomes/genbank or genomes/refseq path on the genomes FTP site</div></li></ul><p>Attempts to access assembly reports using the genomes/ASSEMBLY_REPORTS/All path will fail after the transition period.</p><p>Additional information about the genomes FTP site can be found in the <a href="https://ftp.ncbi.nlm.nih.gov/genomes/all/README.txt" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">genomes FTP README file</a> and in the <a href="https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">genomes FTP FAQ</a>.</p><p>Subscribe to the <a href="https://www.ncbi.nlm.nih.gov/mailman/listinfo/genomes-announce" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">genomes-announce mail list</a> to be informed of changes to the NCBI genomes FTP site.</p></div></div></div><div id="news_08-29-2016-dbvar-july-release"><h2 id="_news_08-29-2016-dbvar-july-release_">dbVar July 2016 data release includes new 1000 Genomes Phase III structural variants</h2><p>
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<i>Monday, August 29, 2016</i>
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</p><p>The <a href="https://www.ncbi.nlm.nih.gov/dbvar/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">dbVar</a> July 2016 data release includes 1,455,032 new Variant regions, 13,961,956 Variant calls and 6 new studies. See a list of the studies, including descriptions and links to the data in the <a href="ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/release_notes/2016_08_09.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">release notes</a>.</p><p>Follow the dbVar <a href="https://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=dbvarnews" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">RSS feed</a> for monthly releases.</p></div><div id="news_08-25-2016-downloading-genome-ftp"><h2 id="_news_08-25-2016-downloading-genome-ftp_">August 31st NCBI Minute: Downloading Genome Data from the NCBI FTP Site</h2><p>
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<i>Thursday, August 25, 2016</i>
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</p><p>In the next NCBI Minute, we will teach you how to use the Web and the command line to quickly access and download genomic sequence and annotation files for a species, metagenome or taxonomic group of interest.</p><p><b>Date and time:</b> Wednesday, August 31, 2016 12:00 PM EDT</p><p><b>Registration URL:</b>
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<a href="https://attendee.gotowebinar.com/register/8835228315982188801" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://attendee.gotowebinar.com/register/8835228315982188801</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="/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_08-23-2016-vastplus-update"><h2 id="_news_08-23-2016-vastplus-update_">VAST+ update provides refined alignments</h2><p>
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<i>Tuesday, August 23, 2016</i>
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</p><p>The new version of <a href="https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">VAST+</a> provides a <a href="/Structure/vastplus/docs/vastplus_help.html#AlgorithmAlignmentRefined" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">refined structure-based alignment</a> of similar macromolecular complexes and displays the 3D superpositions in the <a href="/books/n/newsncbi/N2016-05/?report=reader#news_05-13-2016-icn3d-new-3dviewer">recently launched iCn3D</a>.</p><p>See the <a href="https://www.ncbi.nlm.nih.gov/Structure/MMDB/docs/mmdb_news.html#VASTplus_refined_alignments" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">MMDB news page</a> for more detail about how VAST+ now works.</p></div><div id="news_08-22-2016-edirect-nlm-class"><h2 id="_news_08-22-2016-edirect-nlm-class_">September 12th class at NLM: EDirect - Command Line Access to NCBI's Biomolecular Databases</h2><p>
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<i>Monday, August 22, 2016</i>
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</p><p>On September 12, 2016, NCBI staff will discuss EDirect in a class at the <a href="https://www.nlm.nih.gov/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">National Library of Medicine</a>. During the optional first hour of this workshop (9-10 AM), you will get a basic introduction to the Unix/Linux command line interface. The main workshop (10 AM - Noon) will cover how to use EDirect to set up simple pipelines to retrieve and process data from <a href="https://www.ncbi.nlm.nih.gov/pubmed" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PubMed</a>, <a href="https://www.ncbi.nlm.nih.gov/gene" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Gene</a> and the <a href="https://www.ncbi.nlm.nih.gov/nuccore" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Nucleotide</a> and <a href="https://www.ncbi.nlm.nih.gov/protein" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Protein</a> sequence databases. We will provide access to EDirect installed in a Linux environment on a cloud service.</p><p><b>Date and time:</b> Monday, September 12, 2016 9:00 AM EDT</p><p><b>Registration link:</b>
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<a href="https://www.surveymonkey.com/r/5NCWLK6" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www.surveymonkey.com/r/5NCWLK6</a></p><p>NOTE: This is an in-person class at the National Library of Medicine on the NIH campus in Bethesda, MD, USA. <b>The course is limited to 22 participants. Participants must bring their own laptop.</b></p><p>The EDirect suite of programs allows easy command line access for searching and retrieving literature (PubMed) and accessing NCBI's biomolecular (Gene, Nucleotide, sequence databases, etc.) records. Its advantages include direct command line access to NCBI's databases without writing Perl or Python scripts, construction of custom pipelines for processing data, built-in batch access, and the ability to generate highly flexible custom output reports.</p></div><div id="news_08-11-2016-hiv1-update"><h2 id="_news_08-11-2016-hiv1-update_">HIV-1 datasets in Gene updated</h2><p>
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<i>Thursday, August 11, 2016</i>
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</p><p>NCBI has updated the HIV-1 interaction datasets available in Gene with data provided by the <a href="http://www.southernresearch.org/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Southern Research Institute</a>.</p><p>The <a href="https://www.ncbi.nlm.nih.gov/gene/?term=%22hiv1+protein+interactions%22%5bProperties%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">protein interactions dataset</a> now has:</p><ul><li class="half_rhythm"><div>7,762 interacitons;</div></li><li class="half_rhythm"><div>15,665 interaction descriptions;</div></li><li class="half_rhythm"><div>3,729 proteins encoded by 3,649 human genes;</div></li><li class="half_rhythm"><div>and 6,690 publications.</div></li></ul><p>The <a href="https://www.ncbi.nlm.nih.gov/gene/?term=%22hiv1+replication+interactions%22%5bProperties%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">replications interactions dataset</a> now has:</p><ul><li class="half_rhythm"><div>1,325 interactions;</div></li><li class="half_rhythm"><div>1,439 interaction decriptions;</div></li><li class="half_rhythm"><div>1,325 proteins encouded by 1,325 human genes;</div></li><li class="half_rhythm"><div>and 125 publications.</div></li></ul><p>Data are also available at the <a href="https://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">RefSeq HIV-1 website</a> and the <a href="ftp://ftp.ncbi.nih.gov/gene/GeneRIF" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">GeneRIF FTP site</a>.</p></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK431035_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, August 2016.<span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/newsncbi/N2016-09/?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/N2016-07/?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></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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