[Bioperl-l] StandAloneBlast.pm question

Bin Qian Bin Qian" <bqian@umich.edu
Fri, 26 Oct 2001 10:42:57 -0400


To save time on n.r. database loading, you may want to have a loop to write
all your in_$i.seq into one file, end the loop, then call "blastall" only
once. This way you can parse the result.out all in a time, too.

Hope this helps.


----- Original Message -----
From: "Andrew Emerson" <a.emerson@cineca.it>
To: <bioperl-l@bioperl.org>
Sent: Friday, October 26, 2001 9:18 AM
Subject: [Bioperl-l] StandAloneBlast.pm question

> Dear All
> I am using a (non-bio) perl program which uses the system command to run
> the locally installed NCBI blast:
> ....
> <sequence preparation code>
> system("blastall -p blastn -d /databases/chr1.nt  -q -15  -e 1e-50  -i
> in_$i.seq
> -o results_$i.out");
> <results analysis code>
> .....
> In some cases the system call is in a loop and called many tens of
> thousands of times, resulting in long execution times as a result of
> repeatedly loading the nucleotide database by Blast.
> Can  StandAloneBlast.pm be of any use or does it just effectively work
> the system call? Is there any way in BioPerl to perform a very large
> of Blast searches efficiently or will I be forced to get my hands dirty
> with C and call the Blast functions directly?
> thanks in advance for any help or advice
> Andy Emerson
> ------------------------
> Dr Andrew Emerson
> CINECA (High Performance Systems)
> via Magnanelli, 6/3
> 40033 Casalecchio di Reno (BO)-ITALY
> tel: +39-051-6171653, fax: +39-051-6132198
> e-mail: a.emerson@cineca.it
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