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General Research Use collection streamlines access to patient-level data in dbGaP
In response to many requests from dbGaP users to simplify and streamline the data access request process while respecting patient consent, dbGaP staff have identified “General Research Use” individuals from different studies and created a collection that allows users to access data on these individuals through a single access request.
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Genome Workbench 2.8.10 available
Genome Workbench 2.8.10 is available, as of January 16th. New features include added support for Ubuntu 14.04 and automatic project save. For the full list of fixes, improvements and features, see the Genome Workbench release notes.
Conserved Domain Database (CDD) version 3.13 now available online and via FTP
Conserved Domain Database (CDD) version 3.13 is now available with 286 new or updated NCBI-curated domains and 50,415 total domain models from CDD’s database providers: Pfam, SMART, COG, TIGRFAMs, Protein Clusters, and the NCBI in-house curation project.
NCBI support for SOAP E-Utility ends July 1, 2015
On July 1, 2015, the NCBI E-Utility SOAP web service, along with the SOAP web service for BLAST, will no longer be supported by NCBI. Any requests to these services after that date will not function.
GenBank surpasses one trillion total bases of publicly available sequence data
Last October, GenBank (Release 204) exceeded an astounding 1 Terabase of assembled sequence data.
Nucleic Acids Research Database 2015 Issue illustrates NCBI databases, updates and future plans
The 22nd annual edition of the Nucleic Acids Research Database Issue features nine papers from NCBI staff that present recent updates to our databases, including GenBank, Gene, and RefSeq.
NCBI YouTube channel: A million views and counting!
As of December 31, 2014, we have passed the 1 million mark for lifetime views on our YouTube channel! The NCBI YouTube channel provides presentations and tutorials about our biomolecular and biomedical literature databases and tools.
NCBI's next webinar is The Statistics of Local Pairwise Sequence Alignment, Parts 1 and 2
On Thursday, January 22nd, Stephen Altschul of NCBI will present the first part of a discussion of the statistical theory for local sequence alignments like those produced by the BLAST database search programs. It will cover the statistical parameters for local alignment scoring systems, and the formulas for calculating bit scores and asymptotic E-values and p-values from raw alignments scores.
E-Utilities users: Keep up to date with changes via the Gene database RSS feed
If you use E-Utilities/ESummary with the Gene database and have not subscribed to the Gene News RSS feed, you probably missed an important announcement about a few impending changes:
RefSeq release 69 available on FTP
The full RefSeq release 69 is now available on the FTP site with 74 million records describing 52,276,468 proteins, 9,973,568 RNAs, and sequences from 51,661 organisms.
NCBI annotates 200th eukaryote
The NCBI Eukaryotic Genome Annotation Pipeline has passed a new landmark: the completion of the annotation of 200 different organisms including 76 mammals, 51 birds, 26 other vertebrates, 21 invertebrates and 26 plants. Over half of these were annotated with the help of RNA-Seq evidence available in the Sequence Read Archive. The lucky 200th organism is a fish, the large yellow croaker (Larimichthys crocea). See the full list of annotated organisms here, and request the annotation of your favorite!
NCBI staff will attend International Plant and Animal Genome Conference XXIII
Next week, NCBI staff will present posters and lead a workshop at the International Plant and Animal Genome Conference. In addition, NCBI will have a booth (Booth 618). Staff will be at the booth to answer any questions you may have.
NCBI webinar A Submitter's Guide to GenBank, Part 2 on January 7th
On January 7th, NCBI will present the continuation of the December 17th webinar on using BankIt for GenBank submissions. Part 2 will cover how to use BankIt file inputs to complete a submission of a single or a few nucleotide sequences that require multiple features for each sequence. We will also describe how to create and use Feature Table files to add information about sequence data.