Hi. This is not an answer. I just wanted to comment that there is a CPAN module (or rather a suite of them) called bioperl (there is even a website). I am always curious why i see lots of questions like this, but no recommendations to use bioperl. I can say for the record that i have tinkered with bioperl just a bit, and it is very complex (as this pdf file can attest). However, if i were doing DNA comparisons and such on a regular basis, i would most certainly put aside some time to learn how to use bioperl instead of rolling my own solutions. At least until i had a good feel for it.

jeffa

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)