Position-Specific Iterated BLAST (PSI-BLAST) is 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. For details, see Section 7.1 at the end of this chapter.
An example of PSI-BLAST command-line entry:
blastpgp -i queryfilename -B alignmentfilename -j 2 -d databasefilename
where -j 2 indicates to search for 2 rounds.
Most BLAST options can be used with PSI-BLAST. However, there are several blastpgp parameters specifically for PSI-BLAST. The following table summarizes these PSI-BLAST options.