patmatdb takes a protein motif and compares it to a set of protein sequences.

Here is a sample session with patmatdb:

% patmatdb
Search a protein sequence with a motif
Input sequence(s): sw:*
Protein motif to search for: st[ty]s
Output file [5h1d_fugru.patmatdb]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA

[-motif] (string)

Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example: [DE](2)HS{P}X(2)PX(2,4)C means two Asps or Glus in any order followed by His, Ser, any residue other than Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys. The search is case-independent, so AAA matches aaa.

[-outfile] (report)

Output report filename.