How to extract fasta from a blastdb

Question

How to extract the sequence used to create a blast database. This is useful when you download a blastdb from somewhere else e.g. one of the databases provided by NCBI including the 16SMicrobial database. Or alternatively, when you want to double check which version of a sequence you have included in a blastdb.

Answer 1

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