Extract fasta from blast DB

Posted on March 18, 2014  •  1 minutes  • 71 words  •  Suggest Changes

This will save google some monthly data from me, so here goes. Dumping a blastDB to fasta format :

fastacmd -d BLASTDB -D 1 > blast_db_dump.fasta

(1 for fasta, 2 GI list, 3 accession.version list)

I also found another method, but I don’t have the tool “blastdbcmd”. So maybe you might use :

blastdbcmd -db my_blast_db -entry all > blast_db_dump.fna

Also see this reference. For information about blastdbcmd, see this reference.