From: Mark Thomas <mark@...>
Date: 2009-10-16T11:15:09+09:00
Subject: Re: matching against a zillion patterns


>  Robert, let me disclose some more information about the nature of the
> problem. Actually I have Protein  sequences (strings of variable length
> composed of a 20 letter alphabet) for example "CAARGNDLYSKNIG" can be
> considered as a protein sequence. basically it's just a string.

Have you looked at the BioRuby project? They may have classes that can
help.
http://bioruby.org/