[Bioperl-l] which one and how to configure(blastall)

[michael watson (IAH-C)]

Hi Yanfeng

Starting at the beginning, can you tell me which operating system you
are using, as much about the computer as you know, and what it is
exactly you are trying to do :-)

Mick

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of yanfeng
Sent: 28 February 2005 16:05
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] which one and how to configure(blastall)


Hi, 
Sorry to bother you again.
I want to download blast program now
I want to run blast and get blast report.
I donot know which one I should install and how to configure it( is 
that  like " export BLASTDIR=/ data1/blast/ " )
I use
BEGIN {
 $ENV{'BLASTDIR'} =
'/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10/';
}

but it doesnot work.

blast-2.2.10-amd64-linux.tar.gz 
<ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.10/blast-2.2.1
0-amd64-linux.tar.gz> 

blast-2.2.10-ia32-linux.tar.gz 
<ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.10/blast-2.2.1
0-ia32-linux.tar.gz> 

blast-2.2.10-ia64-linux.tar.gz 
<ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.10/blast-2.2.1
0-ia64-linux.tar.gz> 



My perl script
//
use Bio::SeqIO;
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
$seqio_obj = Bio::SeqIO->new(-file => 'mun_lab.fasta',
                           -format => 'fasta' ); # to wrtie the sequence

to afasta file
$seq_obj = $seqio_obj->next_seq;
#print $seq_obj->seq,"\n";
@params = (program  => 'blastn',
         database => 'db.fa' );
$blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
$report_obj = $blast_obj->blastall($seq_obj);
$result_obj = $report_obj->next_result;
print $result_obj->num_hits;
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