[Bioperl-l] problems with clustalw

nisa_dar vdar at yorku.ca
Fri May 9 21:10:23 EDT 2008


Hi,

I need to do multiple sequence alignments of DNA sequences by using Bioperl.
I am using the following module
Bio::Tools::Run::Alignment::Clustalw;
and I am getting the following error message



Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains:
/share/iNquiry/perl/lib/5.8.5/x86_64-linux-thread-multi
/share/iNquiry/perl/lib/5.8.5
/share/iNquiry/perl/lib/x86_64-linux-thread-multi
/share/iNquiry/perl/lib/5.8.4 /share/iNquiry/perl/lib/5.8.3
/share/iNquiry/perl/lib/5.8.2 /share/iNquiry/perl/lib/5.8.1
/share/iNquiry/perl/lib/5.8.0 /share/iNquiry/perl/lib
/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/5.8.5
/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.4/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.3/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.2/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.1/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.0/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4
/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2
/usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
/usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.4/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.3/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.2/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.1/x86_64-linux-thread-multi
/usr/lib64/perl5/vendor_perl/5.8.0/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4
/usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2
/usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0
/usr/lib/perl5/vendor_perl .) at mult_align.pl line 9.
BEGIN failed--compilation aborted at mult_align.pl line 9.




Here is the piece of code that gives this message

#!/usr/bin/perl -w

use Bio::SeqIO;
use Bio::Align::AlignI;
use Bio::AlignIO;
use Bio::AlignIO::msf;
use Bio::SimpleAlign;
use Bio::PrimarySeq;
use Bio::Tools::Run::Alignment::Clustalw;

use Bio::Root::IO;
use Bio::Seq;


my $query_string =
"tatgtggctggcgagacacgacacttcatatggttttacctctacgtttgagtaattaagtacaatgagctatcact";
my $hit_string =
"tatgtggctggcgagacacgacacttcatatggttttacctctacgtttgagtaattaagtacaatgagctatcact";
my $hit_string_two =
"tatgtggctggcgagacacgacacttcatatggttttacctctacgtttgagtaattaagtacaatgagctatcact";

my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

my $ktuple = 2;
$factory->ktuple($ktuple);

my $seq_obj_on = Bio::Seq->new(-id =>"thal", -seq =>"$query_string");
my $seq_obj_too = Bio::Seq->new(-id =>"lyrata", -seq =>"$hit_string");
my $seq_obj_thre = Bio::Seq->new(-id =>"boechera", -seq
=>"$hit_string_two");

my @seq_array = qw/$seq_obj_on $seq_obj_too $seq_obj_thre/;
my $seq_array_ref = \@seq_array;
my $aln = $factory->align($seq_array_ref);


I would appreciate if anyone could help. I don't know how to supply the
environment variables at unix so if this is the solution please explain how
can I do that. Thanks! 
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