dbSNP build 152 uses SPDI variant notation


dbSNP build 152 is a small incremental update from build 151 provided for you to begin testing and integrating the new build products into your workflow. Build 152 uses the new system with SPDI variant notation and is now available on FTP and the new RefSNP webpage.

The release notes have more information about what’s new in build 152. If you have any questions or comments, send us an email.

Join NCBI at PAG in San Diego, January 12–16, 2019


Next week, NCBI staff will attend the Plant and Animal Genome (PAG) Conference. We have several activities planned, including 1 booth (#223), 4 workshops, 1 talk and 2 posters.

Read on to learn more about what you can look forward to if you’re attending PAG this year. (Note: The listed times are Pacific time.)

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Apply now to join the Seattle Biological Data Science FHackathon February 4-6, 2019


From February 4-6, 2019, the NCBI will help with a data science hackathon at the Fred Hutchinson Cancer Research Center in Seattle. To apply, complete this form (approximately 10 minutes to complete). Initial applications are due Friday, January 11th by 11 pm ET.

The hackathon will focus on genomics as well as general data science. This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.

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BLAST+ 2.8.1 with New Databases and Better Performance


BLAST+ 2.8.1 is now available for download from our FTP site. This the first production release of standalone BLAST to support the new BLAST v5 databases (BLASTDBv5), which are also now available. The new databases have taxonomy information for the database sequences built-in.  This gives you the following important advantages over the v4 databases.

  1. The ability to limit your search by taxonomic group — species level as well as higher taxa.
  2. Improved performance when limiting BLAST search with accessions.
  3. Retrieval of sequences by taxonomic group from a BLAST database with blastdbcmd.

There are some additional enhancements to the search program options.

  1. A new option (-subject_besthit) culls HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another HSP. This is an experimental option and is subject to change.
  2. Use of the -max_target_seqs option for formats 0-4 is now allowed. The number of alignments and descriptions will be set to the max_target_seqs.
  3.  BLAST now issues a warning  about the possibility not seeing all equivalent matches if -max_target_seqs is set to less than five.

The new release also includes a few bug fixes.  Please see the release notes for additional details and, as always, write to us at blast-help@ncbi.nlm.nih.gov with any questions.

Virus Hunting Data Science Hackathon next week in San Diego


From January 9th – 11th, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University. We reached out to the global computational biology and virology community as part of this effort to make data more accessible.

The hackathon teams look forward to leveraging metagenomic datasets in the cloud to find data based on organismal content and update taxonomy – but most of all – hunt down new viruses!

Follow along with the event with NCBI tweets and see our work on GitHub.

Update single records easily with ClinVar’s Single SCV Update


The ClinVar Team is happy to announce a new online form in the ClinVar Submission Portal, the Single SCV Update, which makes it easier for you to update a single record.

ClinVar_SIngle_SCV_2The new ClinVar Single SCV Update form showing the sections for editing the evaluation date, clinical significance, condition, and citations.

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