I really like these bioinformatics problems. :) They look deceptively simple, complicated only by the sheer size of the dataset. You are not the only "gene hunter" here at the Monastery.

As you are a green Perl hacker, I recommend two things:

1) Hang out here a lot. Share in the glow of our collective wisdom. Do a Super Search here in the Monastery for "DNA" (or even a short sequence like "agtc"!)and see what others who have gone before you have learned.

2) Get yourself a good Perl bioinformatics book. A quick search on Amazon yielded about a dozen or so. I have no idea which are worthwhile and which are junk, but I'm sure you are in a better position to judge. And, if in doubt, the O'Reilly books are usually a safe bet.