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 www.ncbi.nlm.nih.gov. 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. The original FASTA file is no longer needed for the BLAST runs. FormatDB may be obtained with the other BLAST binaries from the executables directory (see above). The input for FormatDB may be either ASN.1 or FASTA. Use of ASN.1 is advantageous for those sites that might also wish to format the ASN.1 in different ways, such as a GenBank report. Usage of FormatDB may be obtained by executing FormatDB and a dash.

References
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
Karlin, Samuel and Stephen F. Altschul (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87:2264-68.
Karlin, Samuel and Stephen F. Altschul (1993). Applications and statistics for multiple high-scoring segments in molecu- lar sequences. Proc. Natl. Acad. Sci. USA 90:5873-7.