I don't have much time right now, so just a few general responses in no particular order.

... comment similarly on a thread about K-mers. (BioMonks vs PerlMonks.)

What I mean to convey by such comments is that while I and all (?) of my fellows in this place are biological (as opposed to silicon- or whatever-else-based) Monks, I and many others are not well versed in biological and molecular biological lore. So when someone starts posting about K-mers, consensus sequences, hairpin sequences, etc., etc., I must set off on a little research program that may quickly run into a TL;DR limit. It's always best to post links to explanations of the terms used. E.g., [wp://Consensus sequence] for Consensus sequence. See What shortcuts can I use for linking to other information?. (Although the given link seems too verbose; a more focused definition might be better.)

... I found a couple of tools in 5.10 plus that looked useful, but alas I am stuck with what I have ...

What version(s) of Perl do you have available to you?

I'm still trying to wrap my head around an understanding of the effect of the database in the operations you describe, and just what you are ultimately trying to achieve. Maybe I'll have time for more later.