I wrote a simple program for something similar once. Seemed like you needed to account for inexact matches, if it was a real world and not an academic problem.

You might want to look at the CPAN module String::Approx. It aint a speed demon, but it seemed to work.

http://search.cpan.org/author/JHI/String-Approx-3.20/Approx.pm

Please forgive if I am wrong, I know a little Perl and even less Genetics.

In reply to Re: Re: BioInformatics - polyA tail search by Arbogast
in thread BioInformatics - polyA tail search by MiamiGenome

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