If you want my honest opinion, I think the work of bioinformaticians is important, especially if it has anything remotely to do with curing some disease that my shorten MY life.

So, I recommend that you go to your boss and tell him you either need a faster computer OR you need yet another computer.

I think it is a waste of your precious time to be learning how to coax Perl to use multiple threads. Your time is better spent on doing what you do best: bioinformatics.

Oh, and keep us informed.