[Bioperl-l] module for 6 reading frames

[Brian Osborne]

Chen Li,

There's some documentation on translate() in bptutorial:

http://bioperl.org/Core/Latest/bptutorial.html

You could also use the translate_6frames() method of Bio::SeqUtils.


Brian O.


On 5/16/06 4:52 PM, "smarkel at scitegic.com" <smarkel at scitegic.com> wrote:

> 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
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>>> 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
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>> 
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