[Bioperl-l] Getting nucleotide seq from protein accession

[Stefan Kirov]

Kat,
If you are familiar with Bioperl it is kind of easy-
look at Bio::DB::GenPept (I suppose you use GenPept/GenBank?) on how to 
get the protein record
Go through the dblinks and find the appropriate accession number (where 
the database method returns  GenBank).
Then retrieve this accession number(s) through Bio::DB::GenBank. If you 
are not familiar with Bioperl- read the docs for Bio::DB::GenPept, 
Bio::DB::GenBank, Bio::Annotation and Bio::Annotation::DBLink).
Hope this helps,
Stefan

Kat Hull wrote:

> Hi there,
> I was wondering whether anyone has a solution to my problem. I have a 
> list of protein assession numbers and want to retrieve the 
> corresponding nucleotide sequences automatically.  I thought it would 
> be possible to do this by changing the NCBI url, but this doesn't seem 
> to be the case.
> Is there a bio-perl module that can do this?
>
> Kind regards,
> Kat
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l


Stefan