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.

• What's New