[Bioperl-l] module for 6 reading frames

smarkel at scitegic.com smarkel at scitegic.com
Tue May 16 16:52:05 EDT 2006


Li,

You can either do the substring, and reverse complement, yourself
or you can use the translate() function in Bio::PrimarySeq.  It
inherits from Bio::PrimarySeqI, so check there for the documentation.
That translate() function takes a "-frame" argument.

Scott

PS In future, please respond to the list.  That way others see
the questions and answers.

chen li <chen_li3 at yahoo.com> wrote on 16.05.2006 13:04:36:

> Dear Dr. Markel,
> 
>     I browse through the document of 
> Bio:Tools::Codontable and find this line:
> 
> my $translation= $CodonTable->translate($seq);
> 
> I think this line is to do the translation. Here is my
> question: which line in the doc says how to translate
> the remaining frames 2,3, and -1, -2, -3? 
> 
> 
> Thank you,
> 
> Li
> 
> --- smarkel at scitegic.com wrote:
> 
> > Li,
> > 
> > Use the translate() function in
> > Bio::Tools::CodonTable.
> > 
> > Scott
> > 
> > Scott Markel, Ph.D.
> > Principal Bioinformatics Architect  email: 
> > smarkel at scitegic.com
> > SciTegic Inc.                       mobile: +1 858
> > 205 3653
> > 10188 Telesis Court, Suite 100      voice:  +1 858
> > 799 5603
> > San Diego, CA 92121                 fax:    +1 858
> > 279 8804
> > USA                                 web: 
> > http://www.scitegic.com
> > 
> > 
> > bioperl-l-bounces at lists.open-bio.org wrote on
> > 16.05.2006 07:55:51:
> > 
> > > Hi all,
> > > 
> > > I wonder which module is available for translating
> > DNA
> > > sequence into 6 reading frames.
> > > 
> > > Thank you,
> > > 
> > > Li
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
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