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:

[-infile] (infile)

Profile or matrix file.

[-sequence] (seqall)

Sequence database USA.

[-outfile] (outfile)

Output filename.