Prepare bases for BLAST search.

BLAST is a service of the National Center for Biotechnology Information (NCBI). A nucleotide or protein sequence sent to the BLAST server is compared against databases at the NCBI and a summary of matches is returned to the user.

The www BLAST server can be accessed through the home page of the NCBI at Stand-alone BLAST binaries can be obtained from the NCBI FTP site.

FormatDB should be used to format the FASTA databases for both protein and DNA databases for BLAST 2.0. This must be done before blastall or blastpgp can be run locally. The format of the databases has been changed substantially from the BLAST 1.4 release. A major improvement in this format over the old one is that ambiguity information for DNA sequences is now retrieved from the files produced by FormatDB, rather than from the original FASTA file.