Hello pdahal,

To be honest I never used Perl for this kind of area, so I can not really say that I know how assist you. I did a very short research though and I found this question (translating multiple DNA sequence to protein sequence).

Well although the question may not be what you are looking for, but a fellow monk (polypompholyx) proposes to use BioPerl which I think is what you should work on and possible resolve many problems on the future.

Here is also a nice tutorial (Perl and Bioinformatics).

Hope this helps.