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)