[Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"
haralds_listen at gmx.de
Wed Mar 1 10:44:18 EST 2006
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
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
(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:
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;
(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
[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
With kind regards,
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