Bioperl clustalw Vs Online clustalw

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Bioperl clustalw Vs Online clustalw

Anil Kumar
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);

                                   }

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online.aln.txt (16K) Download Attachment
out.aln (18K) Download Attachment
seq1.fasta (9K) Download Attachment
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Re: 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 <[hidden email]> 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>_______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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