bioinformatics BLAST Create a DNA blastdb


In order to compare query sequences against reference sequences, you must create a blastdb of your reference(s). This is done using makeblastdb which is included when you install blast.

makeblastdb -in <input fasta> -dbtype nucl -out <label for database>

So if you had a file reference.fasta containing the following records:


You would run the following:

makeblastdb -in reference.fasta -dbtype nucl -out my_database

This would create the following files:

  • my_database.nhr
  • my_database.nin
  • my_database.nsq

Note, the database files are labelled with the -out argument.