Pattern Hit Initiated BLAST (PHI-BLAST)
PHI-BLAST (Pattern-Hit Initiated BLAST) is a search
program that combines matching of regular expressions
with local alignments surrounding the match.
The most important features of the program have been
incorporated into the BLAST software framework
partly for user convenience and partly so that
PHI-BLAST may be combined seamlessly with PSI-BLAST.
Other features that do not fit into the BLAST framework
will be released later as a separate program and/or
separate Web page query options.
One very restrictive way to identify protein motifs
is by regular expressions that must contain each instance
of the motif. The PROSITE database is a compilation of
restricted regular expressions that describe protein motifs.
Given a protein sequence S and a regular expression pattern P
occurring in S, PHI-BLAST helps answer the question:
What other protein sequences both contain an occurrence of P
and are homologous to S in the vicinity of the pattern occurrences?
PHI-BLAST may be preferable to just searching for pattern occurrences
because it filters out those cases where the pattern occurrence is
probably random and not indicative of homology.
PHI-BLAST may be preferable to other flavors of BLAST because
it is faster and because it allows the user to express
a rigid pattern occurrence requirement.