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:

[-sequence] (seqall)

Sequence database USA.

[-infile] (infile)

Profile or matrix file.

-gapopen (float)

Gap opening coefficient.

-gapextend (float)

Gap extension coefficient.

[-outfile] (outfile)

Output filename.