profit takes a simple frequency matrix produced by prophecy and uses it to find matches in the input sequence(s) you are searching.
Here is a sample session with profit:
My aligned set of sequences:
% more m.seq >one DEVGGEALGRLLVVYPWTQR >two DEVGREALGRLLVVYPWTQR >three DEVGGEALGRILVVYPWTQR >four DEVGGEAAGRVLVVYPWTQR
Make a simple frequency matrix using prophecy:
% prophecy Creates matrices/profiles from multiple alignments Input sequence set: m.seq Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: Enter a name for the profile [mymatrix]: Enter threshold reporting percentage : Output file [outfile.prophecy]:
Search using profit:
% profit Scan a sequence or database with a matrix or profile Profile or matrix file: outfile.prophecy Input sequence(s): sw:* Output file [outfile.profit]: