PHI-Blast and regular expression matching.

PHI-Blast


        By filling in the "regular expression" box on the PSI-blast page, you can execute a PHI-blast search.
PHI-blast enforces the presence of a motif in addition to the usual PSI-blast criteria for matching.  An example of a regular expression is W-x(9,11)-[VFY]-[FYW]-x(6,7)-[GSTNE]-[GSTQCR]-[FYW]-x(2)-P.  This means a W followed by 9 to 11 of anything, followed by one of the residues V, F, or Y, etc.  The rules for writing regular expressions are explained on the regular expression help page from NCBI. Regular expressions can be used to confine the results to a formally defined family.  A database of defined motifs can be found at PROSITE (http://expasy.cbr.nrc.ca/prosite/).  The motif above is from the PROSITE example page giving the WW domain motif as an example.

    PHI-Blast can also be executed from the Psi-Blast page of the local NetBlast implementation, or from the command line (program blastpgp).  See the local blast help file.
 

Plain regular expression searching.

        One can also use the PROCITE search tools at EXpasy (http://expasy.cbr.nrc.ca/tools/scnpsite.html) to search against the pattern of motifs alone.  Regular expression searching can also be done at PIR. Finally, the seedtop program from the local blast suite can be used to do regular expression searching from the command line on bioinf.  One difference between PHI-Blast and a plain motif search is that the general homology enforced by the PSI-blast part of the algorithm is expected to reduce the incidence of chance matches.


Last update 3/32/2003 - Steve Hardies