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]: