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

[Greg Slodkowicz]

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> 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> 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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