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Tuesday, October 4, 2016
Consensus Coding Sequence (CCDS) release 20 compares NCBI's Homo sapiens annotation release 108 to Ensembl's release 85, and is now available in Gene. This update adds 1,158 new CCDS IDs and 98 genes into the human CCDS set. CCDS release 20 includes a total of 32,524 CCDS IDs that correspond to 18,892 GeneIDs.
Friday, September 30, 2016
On October 11th, the NCBI Minute will be a discussion of changes made to the BLAST standalone distribution due to the switch to HTTPS and the transition of the sequence databases to accession.version as the primary identifier.
Friday, September 30, 2016
The new version of the BLAST+ executables offers support for HTTPS, accession.version as the primary sequence identifier, support for composition-based statistics with RPSTBLASTN, and a new taxonomic organism report. See more details about these updates on BLAST News. A full list of new features, improvements and bug fixes is available in the release notes.
Friday, September 30, 2016
Next Wednesday, October 5th, NCBI staff will give a brief overview of our activities at this year's ASHG meeting related to ClinVar, dbGaP, GRCh38 and other topics, and how these will benefit ASHG attendees.
Thursday, September 29, 2016
Sequence Viewer 3.16 brings several new features, improvements and bug fixes to the graphical viewer, including improved compliance with HTTPS protocol requirements, a new track type, and improved labeling to avoid label duplication. For a full list of changes, see the release notes.
Wednesday, September 28, 2016
GenBank release 215.0 (08/19/2016) has 196,120,831 traditional records containing 217,971,437,647 base pairs of sequence data. In addition, there are 359,796,497 WGS records containing 1,637,224,970,324 base pairs of sequence data, as well as 113,179,607 TSA records containing 103,399,742,586 base pairs of sequence data.
Wednesday, September 28, 2016
The Genomes-announce email list has been reactivated. To sign up for the Genomes-announce Listserv, go to https://www.ncbi.nlm.nih.gov/mailman/listinfo/genomes-announce.
Friday, September 23, 2016
On Wednesday, September 28th, at 3 PM EDT, NCBI will hold a developers' forum for those who use large amounts of NCBI data. The forum will help us provide you with better access to NCBI data.
Thursday, September 22, 2016
On October 4th, 5th, and 6th, the University of Michigan’s Taubman Health Sciences Library will host a series of NCBI workshops that can also be streamed remotely. The workshops are: Navigating NCBI’s Molecular Data Using the Integrated Entrez System and BLAST, A Practical Guide to NCBI BLAST and EDirect: Command Line Access to NCBI’s Biomolecular Databases. Please see the Taubman Health Sciences Library Remote Site Registration Page for details.
Thursday, September 22, 2016
Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Magic-BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available on the FTP site.
Wednesday, September 21, 2016
We have scheduled another round of HTTPS tests, following up from the initial tests performed on September 15. More information can be found on an NCBI Insights Blog post.
Monday, September 19, 2016
On August 23, Drs. Stephen Bryant and Evan Bolton received the American Chemical Society (ACS) 2016 Herman Skolnik Award for their work in developing, maintaining, and expanding the National Center for Biotechnology Information's PubChem database of chemical substances and their biological activities. The award was presented at the ACS 252nd National Meeting & Exposition in Philadelphia.
Monday, September 19, 2016
Next Wednesday, September 21st, NCBI staff will discuss plans regarding the move to HTTPS-only services. This past week, we conducted the first of a series of HTTPS tests; in this webinar, we will talk about this and future tests that will help all of us prepare for this change. We will also briefly discuss circumstances surrounding proxy services and software dependent upon NCBI software, such as the SRA and C++ toolkits.
Thursday, September 15, 2016
The newest video on the NCBI YouTube channel, Tree Viewer: Display Large Trees, demonstrates a new functionality in Tree Viewer - the ability to display much larger trees.
Wednesday, September 14, 2016
NCBI has released a comprehensive update of all current genome assemblies in the Genomes FTP site, affecting data reported in the /genomes/genbank/, /genomes/refseq/ and /genomes/all/ FTP directories. This update adds nucleotide FASTA sequences of CDS and RNA features computed from the genome sequence, expands the scope of the /genbank/ data to include metagenomes, and more. The FTP content of nearly all "latest" GenBank and RefSeq assemblies was updated to reflect these changes between 5/11/2016 and 6/24/2016.
Monday, September 12, 2016
RefSeq release 78 is accessible online, via FTP and through NCBI's programming utilities. This full release incorporates genomic, transcript, and protein data available as of September 6, 2016 and contains 107,045,797 records, including 70,427,238 proteins, 16,172,490 RNAs, and sequences from 62,739 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.
Monday, September 12, 2016
The latest blog post on NCBI Insights discusses what will happen to existing GI numbers in records now that NCBI is phasing out Sequence GIs.
Thursday, September 8, 2016
NCBI is retiring the Leiden Open Variation Database (LOVD) on September 30, 2016. LOVD has been used to capture information about novel human variants. We encourage past submitters of human genetic variations to LOVD to transfer their information to the ClinVar database.
Wednesday, September 7, 2016
The latest blog post on NCBI Insights presents the new PubMed Journals, the latest experiment from PubMed Labs. PubMed Journals allows you to easily find and browse journals of interest, browse new articles, and more. Learn more about PubMed Journals, try it out, and leave us feedback on the blog post.