[ensembl-dev] Pfam and transmembrane domain coordinates in BiomaRt

[Thomas Maurel]

Dear Greg,

Just to let you know that we will add the domain coordinates to the Ensembl gene and vega marts in our next Ensembl release (e!80).
Please note that the coordinate will be protein based since this is how we calculate and store them in Ensembl. 

Hope this helps,
Regards,
Thomas 
> On 17 Apr 2015, at 15:17, Greg Slodkowicz <gregs at ebi.ac.uk> wrote:
> 
> Hi Thomas,
> Thanks for getting back to me so quickly. That would be great. Currently I obtain these annotations using the Perl API but if they were available in Biomart, I could do all my analysis within R.
> 
> Cheers,
> Greg
> 
> On Fri, Apr 17, 2015 at 10:44 AM Thomas Maurel <maurel at ebi.ac.uk <mailto:maurel at ebi.ac.uk>> wrote:
> Dear Greg,
> 
> I am afraid that domain coordinates are not available in the Ensembl Gene mart at the moment but we are looking into adding this in the future since we already had few requests.
> 
> Thanks a lot for your feedback.
> Regards,
> Thomas
> > On 17 Apr 2015, at 10:35, Greg Slodkowicz <gregs at ebi.ac.uk <mailto:gregs at ebi.ac.uk>> wrote:
> >
> > Hi Ensembl team,
> > I'm trying to fetch Pfam and transmembrane domain annotations using the biomaRt package. I noticed that while there are attributes for the annotations themselves ('pfam' and 'transmembrane_domain'), there seem to be no attributes for the coordinates of these domains. Is there a way to get them?
> >
> > Many thanks,
> > Greg
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> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> 
> 
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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