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

[Aaron J Mackey]

To accomplish your task (library of 1000 sequences vs. a second
library of 1000 sequences), BLAST and similar programs should take
less than a minute or two; you can give BLAST (and now, FASTA as well), an
entire query library of sequences, instead of just one at a time
(ensuring that the library is read only once, instead of 1000 times).
There should be no need for parallel task management at all.

If you do need parallel task management, I'd suggest either the pvm/mpi
versions of the FASTA programs (which have the added feature of being able
to do smart library "self comparisons" in N*N/2 comparisons via the -I
option), or using a task management environment such as "disperse" or PBS.

-Aaron

On Fri, 11 Jan 2002, Bob Mangold wrote:

> 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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-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu