blast is optimized to hell. If you say you are faster in perl under some circumstances, you are doing something that is not comparable ;)

Honestly, it makes not much sense to use perl for huge scientific calculations and even less trying it on multiple CPUs. In C (even without OpenMP), you are magnitudes (much more than 2,4,8 times) faster.

Here are a lot of bioinformatic guys, what do you want to do?