prophet finds matches between a GRIBSKOV or HENIKOFF profile produced by prophecy and one or more sequences. Here is a sample session with prophet: The sequence alignment looks like: % more m.seq >one DEVGGEA-GRLLVVYPWTQR >two DEVGREALGRLL-VYPWTQR >three DEVGGEALGRILVVY-WTQR >four DEVGGEAAGRVLVVYPWTQR Create the profile: % prophecy Creates matrices/profiles from multiple alignments Input sequence set: m.seq Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: g Enter a name for the profile [mymatrix]: Scoring matrix [Epprofile]: Gap opening penalty [3.0]: Gap extension penalty [0.3]: Output file [outfile.prophecy]: Now do the search. % prophet Gapped alignment for profiles Input sequence(s): sw:* Profile or matrix file: outfile.prophecy Gap opening coefficient [1.0]: Gap extension coefficient [0.1]: Output file [100k_rat.prophet]: Mandatory qualifiers:
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