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)