[Bioperl-l] Issues with CLUSTALW

[Fields, Christopher J]

You need to install BioPerl-Run as well as the core BioPerl modules.

chris

On Oct 18, 2011, at 12:00 PM, Sarah Tincher wrote:

> 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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