[Bioperl-l] StandAloneBlast.pm question

Andrew Emerson a.emerson@cineca.it
Fri, 26 Oct 2001 15:18:23 +0200

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 
-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 like 
the system call? Is there any way in BioPerl to perform a very large number 
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