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.
PHI-BLAST (Pattern-Hit Initiated BLAST) is a search program that combines matching of regular expressions with local alignments surrounding the match.
An example of a PHI-BLAST command-line entry:
blastpgp -i queryfilename -k patternfilename -p patseedp
where patseedp indicates the mode of usage.
Most BLAST options can be used with PHI-BLAST. However, the use of the -g F option is forbidden because PHI-BLAST requires gapped alignments.
The syntax for patterns in PHI-BLAST follows the conventions of PROSITE. All PROSITE codes are allowed, but only the ID, PA, and HI codes are relevant to PHI-BLAST.
Here is an example of a pattern:
ID ER_TARGET; PATTERN. PA [KRHQSA]-[DENQ]-E-L>. HI (19 22) HI (201 204)
bl2seq (BLAST 2 Sequences) allows for the alignment of two given sequences.
An example of a bl2seq command-line entry:
bl2seq -p programname -i firstfilename -j secondfilename -o <outputfilenanme>
The following table summarizes the bl2seq options.