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 [75]: 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]: Mandatory qualifiers:
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