[Bioperl-l] no results with standalone tblastn

Hubert Prielinger hubert.prielinger at gmx.at
Mon Feb 6 18:16:01 EST 2006

dear torsten,
I have downloaded all the databases, as you recommended me. And it is 
working, but I don't get any results, if I try it online it works fine.
my result file looks like that:

TBLASTN 2.2.13 [Nov-27-2005]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

         (8 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           3,749,503 sequences; 16,556,997,203 total letters


Sequences producing significant alignments:                Score    
E      (bits) Value

the program code for it looks like that:

#!/usr/local/bin/perl -w
      $ENV{BLASTDIR}= "/home/Hubert/blast/blast-2.2.13/bin";
    $ENV{BLASTDATADIR}= "/home/Hubert/blast/blast-2.2.13/data"; 

use Bio::Tools::Run::StandAloneBlast;
use Bio::Seq;
use Bio::SeqIO;
use strict;

print "Please insert matrix:\t";
my $matrix_STD = <STDIN>;
chomp $matrix_STD;

print "Please insert count:\t";
my $count_STD = <STDIN>;
chomp $count_STD;

# parameters
my $expect_value = 20000;
#my $filter_query_sequence = 'T';
my $one_line_description = 1000;
my $alignments = 1000;
#my $matrix = 'BLOSUM80';
my $gapcost = 10;
my $gapextend = 1;
my $wordsize = 2;
#my $compbasedStat = '1';
#my $count = 1;
# my $strands = 1;

my @params = ('program' => 'tblastn','database' => 'nt');
#my $progress_interval = 100;

my $seqio_obj = Bio::SeqIO->new(
  -file   => "aloneblosum62.txt",
  -format => "raw",

# create factory object and set parameters

my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
print "submitted parameters successfully \n";


print "changed parameters successfully \n";
print "\n";

# get query

while ( my $query = $seqio_obj->next_seq) {
      print "entered while loop \n";
      my $blast_report = $factory->blastall($query);
#      print "$blast_report\n";
      print $query->seq;
      print "\n";


Torsten Seemann wrote:

>>thanks for your quick reply, I have looked up at the ftp server and 
>>there are nt.00 to nt.04. Do I have to download all of them, are there 
>You have to download them all. The "nt" database (actually the index 
>files) is very big, and it is split up into gigabyte (?) parts. Although 
>they are called "nt.00" "nt.01" etc, you still pass "-d nt" to 
>"blastall", because together these parts are one "nt" database. The 
>"blastall" program will automatically use the separate parts; you do not 
>have to join them.
>You should read http://www.ncbi.nlm.nih.gov/BLAST/ to make sure you are 
>using the correct BLAST search for your problem.

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