bioinformatics BLAST Extract fasta sequences from a nucl blastdb


You can extract fasta sequence from a blastdb constructed from a fasta file using blastdbcmd which should be installed when you install makeblastdb.

blastdbcmd -entry all -db <database label> -out <outfile>

If you had a database called my_database which contained the files my_database.nhr, my_database.nsq, my_database.nin and you wanted your fasta output file to be called reference.fasta you would run the following:

blastdbcmd -entry all -db my_database -out reference.fasta