I reckon the optimizations will come soon (at least that's what I gathered from reading the Perl 6 documentation's "Performance" section); now that Perl 6.c is out in the wild, there's less of a moving target, so the implementations can (and apparently are) starting to focus more on squeezing out more performance.

And yeah, proto regexes are pretty sweet, and they seem to be a natural fit for what you're doing. I'm always surprised by how popular Perl seems to be in biology / life sciences, and projects like BioInfo (and BioPerl, of course) are a great reminder as to why that happens to be.