[Bioperl-l] Perl / BioPerl question about tasking and threading

[Bob Mangold]

I'm looking for some information about how I can speed up a script I've
written. Basically I take two list of sequences (1000+ seq on each list) and
try to find matches between the two lists. The problem is to do this I have to
make a call to Blast, Clustal, or some other alignment program. Every time I do
this I'm stuck waiting for a response. While the wait is only a few secs it
eventually adds up to minutes an hours or computing time. More frustrating is
that I'm only using about 2% of my CPU to do this.

What I'm looking for is a way to run many of these searches at the same time
and as the responses come back deal with them. I'm trying to use fork and
Thread within Perl, but what I've done still seems to only do one at a time. Am
I just dreaming, or is there a way to do this? If there is a way please point
me in some direction.
-Bob Mangold

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