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

yanfeng yanfeng at csit.fsu.edu
Mon Feb 28 11:05:12 EST 2005


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-2.2.10-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-2.2.10-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-2.2.10-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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