[Bioperl-l] retrieving gene sequence given protein id

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed May 6 23:56:59 UTC 2009

Hi Daniel,

You should be able to do it with Bio::DB::Eutilities

Or use wget and manually link from protein (gi2088631) to gene:

then link gene to nucleotide:

Or use NCBI eUtils

Or build a pipeline:

NCBI is like Perl, there's always more than one way to do it  :-)

--Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Daniel Webb
> Sent: Wednesday, 6 May 2009 11:22 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] retrieving gene sequence given protein id
> Hi all,
> is there a script or a module with which I could, given the list of protein gi
> or accessions, retrieve corresponding genes from Entrez Gene/GenBank? What I
> would like is sequence of the whole gene in fasta format, with all the introns
> and UTRs.
> I would be grateful for any help
> Dan
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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