[Bioperl-l] Issues with CLUSTALW

Sarah Tincher sarah.tincher at gmail.com
Tue Oct 18 13:00:46 EDT 2011


Hello,

I am new to BioPerl and have no computer science background.  I am taking a
bioinformatics course and I have an assignment to write a BioPerl script to
perform the MSA of a specific six sequences, retrieving the sequences from
NCBI and using CLUSTALW.

This is the script I wrote based on a lecture from my course:

#!usr/bin/perl 
use Bio::DB::GenBank;
use Bio::Tools::Run::Alignment::Clustalw;
$gb = new Bio::DB::GenBank();
$seq1 = $gb->get_Seq_by_acc('NP_000509.1');
$seq2 = $gb->get_Seq_by_acc('XP_508242.1');
$seq3 = $gb->get_Seq_by_acc('XP_537902.1');
$seq4 = $gb->get_Seq_by_acc('XP_001252211.2');
$seq5 = $gb->get_Seq_by_acc('NP_032246.2');
$seq6 = $gb->get_Seq_by_acc('NP_942071.1');
$factory = Bio::Tools::Run::Alignment::Clustalw->new;
@seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6);
$seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
print "$aln\n";

And this is the error that I receive:

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains:
/sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8
/sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin
/Library/Perl/Updates/5.8.8/darwin-thread-multi-2level
/Library/Perl/Updates/5.8.8
/System/Library/Perl/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level
/Library/Perl/5.8.8 /Library/Perl
/Network/Library/Perl/5.8.8/darwin-thread-multi-2level
/Network/Library/Perl/5.8.8 /Network/Library/Perl
/System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .)
at HW3_2.pl line 3.
BEGIN failed--compilation aborted at HW3_2.pl line 3.

I would appreciate any help you can provide.

Thank you,
Sarah Tincher  




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