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

[Greg Slodkowicz]

That's great news! Protein-based coordinates are actually more convenient
for me (and, I suspect, most other people).

Thanks,
Greg

On Thu, Apr 23, 2015 at 3:28 PM Thomas Maurel <maurel at ebi.ac.uk> wrote:

> 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> 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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>>
> _______________________________________________
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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
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
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