How to extract fasta from a blastdb 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.
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 &lt;database label&gt; -out &lt;outfile&gt;


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