prophet scans one or more sequences with the supplied Gribskov or Henikoff profile (produced by prophecy). It writes the the highest-scoring (gapped) alignment for each sequence to file, which includes the score for the match. Gap opening coefficient and gap extension coefficient must be specified.
prophet does NOT use the 'simple frequency matrices' produced by prophecy. If you have a 'simple frequency matrix'you should use the program profit to scan sequences.
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EMBOSS An error in prophet.c at line 110: Unrecognised profile/matrix file format
then you have probably given prophet a 'simple frequency matrix' and not a a GRIBSKOV or HENIKOFF profile produced by prophecy.
If you see something like:
Uncaught exception Allocation Failed raised at prophet.c:147
then you have run out of memory. This will occur if your sequence and/or your profile are large.
prophet allocates space based on the length of the sequence and the size of the profile (8 x seqlen x profilelen)