[Bioperl-l] Bioperl clustalw Vs Online clustalw

[Fields, Christopher J]

By ‘online’, what version is it?  The problem is that there are now three versions of Clustal in active use: ClustalW (v1.8), ClustalW2, and Clustal Omega:

http://www.clustal.org

I would expect results to differ if the versions differ.  I highly suggest using a more recent version of ClustalW if possible.

chris

On May 26, 2014, at 7:15 AM, Anil Kumar <anikng at gmail.com> wrote:

> Hi Forum  Members,
> 
> I have a doubt regarding Bioperl clustalw and it is as follows. If someone
> know the solution, kindly suggest me.
> 
> Using Bioperl (clustalw 1.8V), I successfully aligned multiple sequences
> from a .fasta file and saved it in clustalw format. However, the alignment
> result is different from the  online clustalw result of the same sequences.
> 
> I guess that the change is due to some input parameters, but i failed to
> provide the exact input parameter in order to get the alignment as online
> clustalw.
> 
> 
> 
> Ani Lee
> Seoul, ROK
> 
> Here is my code, (Also sending the input file (seq1.fasta), output file
> (out.aln) and online output (online.aln.txt)
> 
> #!/usr/bin/perl
> BEGIN { $ENV{CLUSTALDIR} = 'C:/clustalw'; }
> 
> 
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::AlignIO;
> 
> 
> $inputfilename = "seq1.fasta";
> $in  = Bio::AlignIO->new(-file   => $inputfilename , ktuple => 2, matrix =>
> BLOSUM, type => dna, extend => 0.1, gapopen => 10, gapext => 0.05,
>                             format => 'fasta');
> 
> 
> 
> $out = Bio::AlignIO->new(-file   => ">out.aln" ,
>                             -format => 'clustalw');
> 
> 
> 
> while ( my $aln = $in->next_aln() ) {
>        $out->write_aln($aln);
> 
>                                   }
> <online.aln.txt><out.aln><seq1.fasta>_______________________________________________
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