Tutorial by Examples: 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 referen...

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_databas...

Data can be extracted from a blastdb using blastdbcmd which should be included in a blast installation. You can specify from the options below as part of -outfmt what metadata to include and in what order. From the man page: -outfmt <String> Output format, where the available format sp...