/ 
Bio-Protease-1.112980
River stage zero No dependents
/ Bio::Protease::Role::Specificity::Regex

NAME

Bio::Protease::Role::Specificity::Regex - A role that implements a regex-based specificity

VERSION

version 1.112980

SYNOPSIS

package My::Protease;
use Moose;

with qw(Bio::ProteaseI Bio::Protease::Role::Specificity::Regex);

package main;

my $p = My::Protease->new( regex => qr/.{3}AC.{3}/ ); # coerces to [ qr/.../ ];

my @products = $p->digest( 'AAAACCCC' );

# @products: ('AAAA', 'CCCC')

DESCRIPTION

This role implements a regexp-based specificity for a class that also consumes the Bio::ProteaseI role. A peptide will be cleaved if any of the regexes provided at construction time matches it. The regexes should be tailored for 8-residue-long peptides, the cleavage site being between the fourth and fifth residues.

For instance, if the specificity could be described as "cuts after lysine or arginine", the appropriate regular expression would be qr/.{3}[KR].{4}/.

ATTRIBUTES

regex

A ProteaseRegex, which is basically an array reference of regular expressions that describe the protease specificity. It can coerce from a single regular expression into a single-element array of regexps. Any of the regexes in the array should match a given substrate for it to be cleavable.

AUTHOR

Bruno Vecchi <vecchi.b gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Bruno Vecchi.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.