Start the program with prosearch filename . The program is thus not so different from the GCG program motifs . Can also be run from the menu system. Pratt Pratt is a program that will attempt to locate conserved motifs within an alignment. The alignment can be in several formats.
Trivial use is supported by the menu system.
The help file is here . Start the program with pratt fasta filename for a fasta format alignment, or pratt gcg filename for a gcg alignment. Important note Pratt is trying to match a set of 'expressions' to your sequence and score them. The menu system will copy this for you if you do not have it already. The point here is that you can define your own patterns to be matched onto alignments.