[Bioperl-l] translating Sequence in 6 open reading frames

[Brian Osborne]

Anika,

In order to get all 6 frames simplify your code, something like:

 my $seqobj = Bio::Seq->new ( -seq => $seq,
   -alphabet  => 'DNA');
 my @seqs = Bio::SeqUtils->translate_6frames($seqobj);


Brian O.


On 12/12/05 10:26 AM, "joecker at freenet.de" <joecker at freenet.de> wrote:

> Hello,
> I try to use BioPerl for the translation of a sequence in 6 reading frames.
> The Sequence is stored in a variable.
> First I create a new Seq object with:
> my $seqobj = Bio::Seq->new ( -seq => $seq,
>   -alphabet  => 'DNA',
> );
> afterwards I use the package Bio::SeqUtils for translating:
> 
>  my $util = new Bio::SeqUtils
> my $polypeptide_3char = Bio::SeqUtils->seq3($seqobj);
> Bio::SeqUtils->seq3($seqobj, $polypeptide_3char);
> my @seqs = Bio::SeqUtils->translate_6frames($seqobj);
> 
> Unfortunately I was not able to create the object. The program stops, but
> there is no error.
> I hope someone can help me.
> 
> Thanks a lot for your help,
> Anika
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