[Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"

Harald haralds_listen at gmx.de
Wed Mar 1 10:44:18 EST 2006

Hi all.

I am a Bioinformatics Newbie and want to use BioPerl for doing BLASTs on 
a local protein-sequence file. Unfortunately something went wrong, which 
gives me the error message: "...Unable to open BLOSUM62...".

I am using Win2000 on a normal Desktop PC with 1.4 GHz AMD and 256 MB 
RAM (I know, this is not much, but my sequence database is not so big).
My perl-interpreter is from ActiveState and in the version 5.8.7 built 
for MSWin32-x86-multi-thread
BioPerl is version 1.4
Blast has version 2.2.13

(1) I have downloaded the blast distribution from 

(2) I have installed it and put the file ncbi.ini into my 
WINNT-directory, which is pointing to blast-directory/data

(3) I downloaded a FASTA-formatted protein-sequence database file 
(ftp://ftp.ncbi.nih.gov/pub/COG/KOG/kyva) [48MB]

(4) I used formatdb -i kyva and received the files kyva.phr, kyva.pin 
and kyva which I put into the directory, where my perl-script resides.

(5) Now I tried to BLAST this database for a sequence, I have copied out 
of it. Therefore I just modified the BLAST-script from the Beginner-HowTo:
use strict;

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

my @params = (program  => 'blastp', database => 'kyva' );

my $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);

my $seq_obj = Bio::Seq->new(-id  =>"test_query", -seq 

my $report_obj = $blast_obj->blastall($seq_obj);

my $result_obj = $report_obj->next_result;

print $result_obj->num_hits;


(6) But if I trigger this script, I receive:
[NULL_Caption] WARNING:  [000.000]  test_query: Unable to open BLOSUM62
[NULL_Caption] WARNING:  [000.000]  test_query: BlastScoreBlkMatFill 
returned no
n-zero status
[NULL_Caption] WARNING:  [000.000]  test_query: SetUpBlastSearch failed.

Does anyone has a clue, what is going wrong? Since my ncbi.ini - file 
points to the directory, where blosum62 is found, I can not understand 
this error-message.

With kind regards,
frustrated Harald

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