[Bioperl-l] Getting nucleotide seq from protein accession
skirov at utk.edu
Thu Jun 23 15:52:58 EDT 2005
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,
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,
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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