Create Blast Databases One for Each Chromosome

Once the genome has been downloaded and the BLAST suite has been installed, create BLAST databases for each of the chromosome FASTA files using the formatdb command line utility. The formatdb command line utility must be used to format a FASTA file such as chr7.fa into a BLAST database before it can be searched by MegaBLAST. The following command is an example of using formatdb to create a BLAST database:

Executing this command will create the files: chr7.fa.nhr, chr7.fa.nin, and chr7.fa.nsq, which collectively represent the BLAST database for mouse chromosome 7. This database will be searched by MegaBLAST in order to produce sequence alignments for the purpose of identifying segmental duplications in the genome. BLAST databases must be created iteratively for every FASTA file for each chromosome sequence in the genome, including the pseudo chromosomes (see Note 8).

In the example above, "-i chr7.fa" specifies the name of the input file, and "-p F" specifies that the sequence contained within the file is nucleotide. Below is a detailed description of the command line options used:

formatdb 2.2.10 arguments: -i Input file(s) for formatting (this parameter must be set) [File In]

-p Type of file T - protein

F - nucleotide [T/F] Optional default = T

A fUll description of this command and its options is included with the documentation supplied with the BLAST suite and is also available at the NCBI website (

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