[ensembl-dev] BIOMART

[Michael Schuster]

Hello Nicholas,

The BioMart variation data sets can be filtered by their association  
with a particular Ensembl gene stable identifier (e.g. ENSG00000146648  
for the human EGFR gene) and directly support the export of flanking  
sequences of a specified length.

While this works fine for the human germ-line variation data set  
(dbSNP 135), the human somatic variation data set (COSMIC 58) suffers  
from a configuration error so that this functionality is currently not  
available. Please accept our apologies for this mistake.

I have been informed that this will be rectified with the next Ensembl  
release.

Best regards,
Michael Schuster


On 17 May 2012, at 10:56, Hickson Nicholas (RW3) CMFT Manchester wrote:

> Dear Sir/Madam,
>
>
>
> I recently attended a seminar in Manchester at the NOWGEN centre,  
> during which Dr Michael K. Schuster gave a presentation about the  
> ENSEMBL browser, including BIOMART.
>
>
>
> I have a question I would like to ask:
>
>
>
> Could you please let me know how I could extract all the somatic  
> mutations for a specific gene (E.g. EGFR) reported on COSMIC,  
> including their genomic reference coordinates, in order to then be  
> able to actually get 200 bp of flanking sequence around the mutation  
> by entering these details into the UCSC browser or the ensembl  
> website if possible.
>
>
>
> Thank you,
>
> Best wishes,
>
>
>
> Nicholas Hickson
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Dr Nicholas Hickson (PhD)
>
> Trainee Clinical Scientist
>
> Regional Genetics Laboratories
>
> Genetic Medicine (6th floor)
>
> Manchester Academic Health Science Centre
>
> St Mary's Hospital
>
> Oxford Road
>
> Manchester M13 9WL
>
> UK
>
> Email: Nicholas.Hickson at cmft.nhs.uk<mailto:Nicholas.Hickson at cmft.nhs.uk 
> >
>
> Tel: 0161 27 63265
>
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--
Michael Schuster, Ph.D.
Ensembl Genome Browser Project
Vertebrate Genomics Team
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD
United Kingdom

http://www.ensembl.org/