[Bioperl-l] retrieving gene sequence given protein id

Daniel Webb webb.daniel at yahoo.com
Thu May 7 04:28:44 EDT 2009

Awesome! Thank you all for replying :)

--- On Wed, 5/6/09, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:

From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
Subject: RE: [Bioperl-l] retrieving gene sequence given protein id
To: "'Daniel Webb'" <webb.daniel at yahoo.com>, "'bioperl-l at lists.open-bio.org'" <bioperl-l at lists.open-bio.org>
Date: Wednesday, May 6, 2009, 11:56 PM

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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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