[Bioperl-l] retrieving gene sequence given protein id

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed May 6 19:56:59 EDT 2009


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&part=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
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