Ncbi command tools for blast+
BLAST+ documentation is available online at http://www.ncbi.nlm.nih.gov/books/NBK1763/
The NCBI BLAST+ is a group of tools for basic alignment search. BLAST+ is a rewrite of BLAST with new features and performance improvements. BLAST+ commands differ from original BLAST. For BLAST users, one should read the BLAST USERS paragraph.
BLAST+ uses the BLASTDB environment variable to get default db directory. It is possible to update the file /etc/ncbi/.ncbirc to add the following: [BLAST] BLASTDB=/var/lib/ncbi-blast+/db
The easiest way to get started using these command line applications is by means of the legacy_blast.pl PERL script which is bundled along with the BLAST+ applications. To utilize this script, simply prefix it to the invocation of the C toolkit BLAST command line application and append the --path option pointing to the installation directory of the BLAST+ applications. For example, instead of using
blastall -i query -d nr -o blast.out use legacy_blast.pl blastall -i query -d nr -o blast.out --path /usr/bin
Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging NCBI - BLAST+