[Bioperl-l] Seq::IO/clustalw

[Brian Osborne]

Liam,

For the details on getting translations of nucleotide sequences when the
input files are EMBL or Genbank format please see the Feature-Annotation HOW
TO. There are different ways to do this but the basic idea is
"$feat_object->get_tag_values('translation'))". First get a SeqFeature
object, then extract data from it. If your input files aren't either of
these formats then it's a different problem.

Brian O.




-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Liam Elbourne
Sent: Sunday, March 28, 2004 9:59 PM
To: BioPerl
Subject: [Bioperl-l] Seq::IO/clustalw

Hi All,

Is there a quick way of substituting protein ids for accession codes.
I've just done an clustalw alignment using DNA, and decided to use the
protein sequences instead (not a very good alignment.......). Rather
than substitute the protein ids manually, I wondered whether at the:

my $seqobj = $db->get_Stream_by_id(['x?????','af?????', etc, etc, etc);

step I could get the corresponding amino acid translation for the
accession?. The sequences then get written to a file which is passed to
clustalw.

     my $seq_out = Bio::SeqIO->new( -format => 'fasta',
                                  -file => "> $outfile");

     while( $aseq = $seqobj->next_seq() )
     {
        $seq_out->write_seq($aseq);
     }


Regards,
Liam Elbourne.

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