[Bioperl-l] Existing bioperl module/function?

[Jason Stajich]

See the example HOWTO Feature-Annotation - if the peptide has a has an  
annotated CDS you can grab that cross-reference from the genbank file  
and then use the Bio::DB::GenBank to retrieve that CDS record.

 From my tutorials you can also see example solution.
With some background here
http://jason.open-bio.org/Bioperl_Tutorials/Duke_2004/ 
BioperlProjects.pdf
and an answer for retrieval from swissprot/EMBL some modification  
needed to get it from GenPept/GenBank.

   
http://jason.open-bio.org/Bioperl_Tutorials/Duke_2004/problem_sets/ 
Project1/get_cds_for_protein.pl

-jason

On Sep 30, 2004, at 6:48 PM, Sun, Jian wrote:

> Dear all;
>    I need some help on this problem: Is there any bioperl module or  
> functions available to be used to get the corresponding nucletide  
> sequence of a certain protein ? Then also can retrive the oligo  
> sequence of a specified peptide segment of this protein sequence?
>
>    At the NCBI site, we can retrieve the both sequences through its  
> protein and nucleotide database seperately and then find the  
> corresponding matches at the certain sequence position. In bioperl, it  
> is possible that I may can use the reverse translation to soluve this,  
> but it leads to the degenerate sequence, not the one to one match of a  
> certain protein.  And I am more interested in the retriving the  
> corresponding nucleotide sequence of the peptide fragment of the same  
> protein.  So I just wonder if there is a more direct way through using  
> the existing bioperl module.
>
> Thanks in advance
> Jian Sun
>
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/