NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria


NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus.

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June 7th NCBI Minute: PubChem: A source of laboratory chemical safety information


On June 7, 2017, NCBI staff will show you how to use PubChem’s Laboratory Chemical Safety Summary (LCSS) to find the most relevant chemical safety information including flammability, toxicity, exposure limits and symptoms, first aid, handling and clean up.

Date and time: Wednesday, June 7, 2017 12:00 PM – 12:30 PM EDT

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 NCBI YouTube channel. Any related materials will be accessible on the Webinars and Courses page; you can also learn about future webinars on this page.

New releases from NCBI: IgBLAST 1.7.0 and Sequence Viewer 3.21


IgBLAST 1.7.0 release

A new version of IgBLAST is now available on FTP, with the following new features:

  1. Specify whether overlapping nucleotides at VDJ junctions are allowed in matching V, D, and J genes.
  2. Set a custom J gene mismatch penalty
  3. Report the CDR3 start and stop positions in the sub-region table
  4. Use alignment length instead of percent identity as the tie-breaker for hits with identical blast scores, improving accuracy in the V, D, J gene assignment.

IgBLAST was developed at the NCBI to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences.

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dbGaP 10th Anniversary Symposium June 9, 2017


dbGaP (the NIH database of Genotypes and Phenotypes) is celebrating its 10th Anniversary this year! We are proud to support over 850 studies and 1.6 million samples.

We invite you to join us at the dbGaP 10th Anniversary Symposium to be held on June 9, 2017; 1:30-3:00 PM Wilson Hall, Building-1 on the NIH Bethesda campus. For information on Campus access and security, NIH Visitor Center, Parking, and directions to NIH, see the NIH Visitor Information page.

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Retiring and replacing the BLink protein similarity service


NCBI is discontinuing the BLink protein similarity service effective immediately. BLink provided graphical access to related proteins from protein records in the Entrez system. Because of the increasing volume of data in the protein database, BLink has become less useful as a tool for finding related sequences and is no longer maintainable.

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QuickBLASTP adds pre-processing to BLAST search


QuickBLASTP, an accelerated version of BLASTP, adds a new pre-processing step to the non-redundant (nr) protein database. In a matter of seconds, QuickBLASTP will find approximately 97% of the database sequences with 70% or more identity to your query and around 98% of the database sequence with 80% or more identity to your query.

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RefSeq release 82 now public


RefSeq release 82 is accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available as of May 8, 2017 and contains 127,098,289 records, including 84,756,971 proteins, 18,901,573 RNAs, and sequences from 69,035 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

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Phasing out support for non-human genome organism data in dbSNP and dbVar


This blog post is directed toward people who use dbSNP and dbVar, particularly those who submit non-human data to the two databases.

dbSNP and dbVar archive, process, display and report information related to germline and somatic variations from multiple species. These two databases have grown rapidly as sequencing and other discovery technologies have evolved, and now contain nearly two billion variants from over 360 species.

Based on projected growth and the resources required to archive and distribute the data, continued support for all organisms will become unsustainable for NCBI in the near future. Therefore, NCBI will phase out support for all non-human organisms in dbSNP and dbVar, and will support only human variation.

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Genome data download made easy!


This blog post is directed toward Assembly users.

A new “Download assemblies” button is now available in the Assembly database. This makes it easy to download data for multiple genomes without having to write scripts.

For example, you can run a search in Assembly and use check boxes (see left side of screenshot below) to refine the set of genome assemblies of interest. Then, just open the “Download assemblies” menu, choose the source database (GenBank or RefSeq), choose the file type, and start the download. An archive file will be saved to your computer that can be expanded into a folder containing your selected genome data files.
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