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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