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

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.