[Bioperl-l] how to map ensembl id to NCBI gi

[Pablo Marin-Garcia]

If you are mapping ensembl genes to NCBI genes (via ensemblaPI or biomart) 
please read this recent thread at ensembl-dev:

http://listserver.ebi.ac.uk/mailing-lists-archives/ensembl-dev/msg05417.html

Seems that the ensembl gene mapping to NCBI is done through translation so 
the noncoding genes do not have the corresponding NCBI gene mapped.


   -Pablo



> ------------------------------
>
> Message: 4
> Date: Wed, 9 Dec 2009 19:59:37 -0600
> From: Chris Fields <cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] how to map ensembl id to NCBI gi
> To: Tom Keller <kellert at ohsu.edu>
> Cc: BioPerl-List <bioperl-l at bioperl.org>
> Message-ID: <14495B1F-911C-4FE7-8224-A3F050F7E03C at illinois.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Tom,
>
> Probably best to do this via BioMart:
>
> http://www.ensembl.org/biomart/
>
> I would assume you can also do this via the ensembl perl API as well.
>
> Also, have a look at the UniProt ID Mapper:
>
> http://www.uniprot.org/?tab=mapping
>
> chris
>
> On Dec 9, 2009, at 6:36 PM, Tom Keller wrote:
>
>> Greetings,
>> Is there a simple way to map a list of ensembl ids to the NCBI gis?
>>
>> thanks,
>> Tom
>>
>> Thomas (Tom) Keller
>> kellert at ohsu.edu
>> 503.494.2442
>> 6339b R Jones Hall (BSc/CROET)
>> www.ohsu.edu/xd/research/research-cores/dna-analysis/
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>

====================================================================
                      Pablo Marin-Garcia, PhD

                     \\//          (Argiope bruennichi
                \/\/`(||>O:'\/\/   with stabilimentum)
                     //\\

Sanger Institute                |  PostDoc / Computer Biologist
Wellcome Trust Genome Campus    |  team : 128/108 (Human Genetics)
Hinxton, Cambridge CB10 1HH     |  room : N333
United Kingdom                  |  email: pablo.marin at sanger.ac.uk
====================================================================


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