Overall help with pratt can be found at the EBI pratt help pages.
A test file is: /users/students4/software/public/Bio4/src/Pratt2.1/test.fasta
You will need to copy this file to your own directory:-
cp /users/students4/software/public/Bio4/src/Pratt2.1/test.fasta ./
You execute a file containing fasta sequences by typing
pratt fasta <input file>
Example:
pratt fasta test.fasta
This generates a menu with parameters (with default values) which can be reset using the appropriate command. The 'CM' and 'C%' commands alter the min number of seqs which are matched.
In their Protein Science paper (1995, 1587-1595) the authors use 'greedy' algorithms at various stages. The 'greedy' parameter can be altered with the 'E' command.
There are several 'Pratt.sets.*' files (e.g. Pratt.sets.big) in the
directory
/users/students4/software/public/Bio4/src/Pratt2.1
which are used to define individual matches. E.g. the first 20 lines are
all single letters (for each of the 20 amino acids). The next lines define
amino acids which share some common properties (e.g. hydrophobicity).
Therefore these lines are vaguely similar to a blosum matrix, allowing
users to define amino acids which (for alignment purposes) can be
considered to be 'allowed' matches.