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

[Nirav Merchant]

You might want to look at megaBLAST
regards,
Nirav
PS: NCBI blast has a option of using multiple processors I think its -a

Mega BLAST uses the greedy algorithm of Webb Miller et al. for nucleotide
sequence alignment search and concatenates many queries to save time spent
scanning the database. This program is optimized for aligning sequences that
differ slightly as a result of sequencing or other similar "errors". It is 
up to
10 times faster than more common sequence similarity programs and therefore can
be used to swiftly compare two large sets of sequences against each other.

At 12:45 PM 1/11/2002 -0800, 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
>
>__________________________________________________
>Do You Yahoo!?
>Send FREE video emails in Yahoo! Mail!
>http://promo.yahoo.com/videomail/
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@bioperl.org
>http://bioperl.org/mailman/listinfo/bioperl-l