But I'm sure there are already much more efficient algorithms out there

No, there aren't.

I can hardly imagine that none of the BioPerl modules already include necessary routines

You've obviously never tried using BioPerl modules. Every one I've tried has been over-engineered, clumsy and dog slow. And those are the good ones, and many are not.

And I'll make you a bet you won't take up.

I bet that you cannot post a BioPerl solution to the OPs problem exactly as stated.

Much less one that will perform better than my solution.

I'm sure ... no need to reinvent the wheel. I can hardly imagine ... IMHO ... very likely

Based upon your extensive experience of all things BioInformatic, and your uncanny ability to second guess the true nature of the OPs task I take it.

IMO, you are wrong on all counts. And until the OP comes and sets the record straight, that is what I will choose to believe.

Just as I will continue to enjoy solving the problems OPs post. Because I enjoy the challenge.

For the record: I find your--if, but, maybe Xy, someone else has probably already solved it if only you changed the problem to suit their solution--attitude, arrogant, patronising and completely unhelpful. Oh And decidedly off-topic.