[Bioperl-l] retrieving gene sequence given protein id

[Daniel Webb]

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
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook 

Or use wget and manually link from protein (gi2088631) to gene:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=protein_gene&from_uid=2088631

then link gene to nucleotide:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_nuccore&from_uid=282375 


Or use NCBI eUtils
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=coursework∂=eutils

Or build a pipeline:
http://www.ncbi.nlm.nih.gov/Class/wheeler/eutils/epipe.html


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, 
Mosgiel, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  
www.agresearch.co.nz 





> -----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
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================