The blastpgp program can do an iterative search in which sequences found in one round of searching are used to build a score model for the next round of searching.

The program aligns sequence (input file) on the base prepared by program FormatDB.

The blastpgp program can do an iterative search in which sequences found in one round of searching are used to build a score model for the next round of searching. In this usage, the program is called Position-Specific Iterated BLAST, or PSI-BLAST. As explained in the accompanying paper, the BLAST algorithm is not tied to a specific score matrix. Traditionally, it has been implemented using an AxA substitution matrix where A is the alphabet size. PSI-BLAST instead uses a QxA matrix, where Q is the length of the query sequence; at each position the cost of a letter depends on the position w.r.t. the query and the letter in the subject sequence.

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.