I am not sure what you are doing, but BLAST: "Basic Local Alignment Search Tool" is a bio "buzzword" and there are a lot of tools to deal with that.

I don't use BioPerl and I really don't know what the possibilities are. But I would start with: Google Perl Blast.

I feel like I'm not using everything Perl has to offer , is probably right! Bio Informatics and Perl fit very well together. Perl can do a lot more than just solve this problem "at hand". I think that you will find more powerful tools than we can present here for the "problem of the day".