Have you ever searched the NCBI Protein database and been overwhelmed with the number of sequences returned? Have you tried searching with a protein name, thinking that would greatly limit the results, only to still be presented with many sequences (all with the same name)? It’s a common problem in this time of greatly expanding sequence databases powered by large-scale genomic sequencing of similar organisms. Redundancy in the sequence databases is high and only getting worse.
To address this, in 2013 NCBI released the WP records, which collect identical protein sequences annotated on bacterial genomes. In 2014, NCBI released the Identical Protein Reports on Protein records, which displays information about all other proteins identical to that protein. Now, we are releasing a new resource: Identical Protein Groups (IPG). IPG offers several features:
ClinVar, NCBI’s archive of submitted associations between alleles in the human genome and diseases or phenotypes, is now producing XML files that aggregate all submitted disease/phenotype information by variant (or set of variants) for public release via FTP bulk download. The new product, called ClinVarVariationRelease, is currently in beta release and will move to full release in early September 2017.
The newest video on the NCBI YouTube channel will show you how to have your PubMed searches automatically run and the results emailed to you daily, weekly or monthly. You will also learn how to create PubMed collections that you can share with others or keep privately for yourself.
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RefSeq release 83 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available as of July 17, 2017, and contains 132,052,465 records, including 88,385,530 proteins, 19,634,664 RNAs, and sequences from 71,356 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings. More information about RefSeq release 83 is available in the release notes.
NCBI will phase out support for non-human organisms in the dbSNP and dbVar databases. These databases will stop accepting submissions for non-human SNPs in September 2017. The interactive websites for these databases and related NCBI services, including RefSeq flatfiles, will stop presenting non-human variant data in November 2017.
The newest video on the NCBI YouTube channel discusses how eligible individuals and journal clubs can join PubMed Commons and contribute comments.
PubMed Commons enables members to post comments about publications, which appear directly below abstracts in PubMed.
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This week, we’ve updated Multiple Sequence Alignment (MSA) Viewer, Tree Viewer, and Genome Workbench . You can see a full list of new features, improvements and bug fixes in each resource’s release notes:
The recording of the June 28th webinar on My NCBI is now on YouTube. In this NCBI Minute, we show you how to automatically highlight keywords, create custom filters that can be active every time you run a search, and permanently display up to 200 items per results page.
The NCBI Minute is a series of short webinars that give a brief introduction to a specific topic or NCBI tool. Learn about future presentations on the Webinars and Courses page.
NCBI usually participates in hackathons as direct organizers and planners. However, NCBI staff recently functioned as facilitators in two hackathons organized by outside groups: one at the Bio-IT World conference, and one at the Silicon Valley Artificial Intelligence (SVAI) incubator.
In June, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms, including Danio rerio (zebrafish):
Would you like to have new PubMed citations for your topic of interest conveniently appear in your email inbox or quickly collect those records for further review? Join NCBI on July 19, 2017, when we’ll show you how to have your PubMed searches automatically run and the results emailed to you daily, weekly or monthly. You will also learn how to create PubMed collections that you can share with others or keep privately for yourself. Don’t have a My NCBI account yet? Get started at MyNCBI.