patmatmotifs takes a protein sequence and compares it to the PROSITE database of motifs.

Here is a sample session with patmatmotifs:

% patmatmotifs -full
Matching Prosite Motif Database to a single sequence.
Input sequence: sw:12s1_arath
Output file [12s1_arath.patmatmotifs]:

Mandatory qualifiers:

[-sequence] (sequence)

Sequence USA.

[-outfile] (report)

Output report filename.

Optional qualifiers:

-full (boolean)

Provide full documentation for matching patterns.

-[no]prune (boolean)

Ignore simple patterns. If this is true, these simple post-translational modification sites are not reported: myristyl, asn_glycosylation, camp_phospho_site, pkc_phospho_site, ck2_phospho_site, and tyr_phospho_site.