bl2seq (BLAST 2 Sequences) allows the blast searching of one sequence against another sequence, without having to run formatdb to create a blast database of the sequence to be searched against.

bl2seq is one of the programs distributed along with the old blastall program by the NCBI. The NCBI recommends that people start using the programs of the blast+ package instead. Having said that, most documentation currently available still refers to blastall and the programs distributed with it.

For further details on bl2seq, type man bl2seq on the command line in a Bio-Linux terminal or refer to the local or remote documentation listed on this page.

The programs distributed with blastall include:

• bl2seq
• blast2
• blastall
• blastcl3
• blastclust
• blastpgp
• copymat
• fastacmd
• formatdb
• formatrpsdb
• impala
• makemat
• megablast
• rpsblast
• seedtop
• taxblast

The man pages for these provide further details.