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.