Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases

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.