Description Takes a protein motif and compares it to a set of protein sequences.
The motif is converted to a regular expression, and matches are completed using Henry Spencer's regular expression library of functions. It returns the number of matches there were between the motif and each matched sequence, length of match, start and end positions of match, and writes out an alignment. Here is a sample session with patmatdb. The search is case-independent, so 'AAA' matches 'aaa'. The search is case-independent, so 'AAA' matches 'aaa'.