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)