I don't know what you are doing, but it almost sounds like you are looking for e.g. bioperl.org?

You might also want to look at Mastering Perl for Bioinformatics from O'Reilly. (That page have a free chapter on the net about Bioperl.)

Update:
Hmm... I looked at your other questions (should have done that before answering, I'm still a newbie).

You are working with DNA sequences. If you are going to do a lot of this (and isn't just trying to get help for a lab!), you probably want to read a book or two. There is a Beginning Perl for Bioinformatics. A good start is to look at O'Reilly.