[ensembl-dev] VEP Interpro ID & description

[Will McLaren]

Hi Guillermo,

Have you tried the --domains flag in the VEP?

Perhaps this is not enough information for you but it does provide the
display label of overlapping protein domains.

The protein object is referred to as a translation object in the Ensembl
API; you can retrieve it from the transcript via $transcript->translation.

See
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html

Regards

Will


On 13 May 2013 12:15, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hello,
>
> So it seems nobody has done this yet. I'll do it then :)
>
> Does VEP support any kind of """Proteinfeature"""? Checking the other
> scripts it seems I must be using Transcript feature_type.
>
> Correct me if I'm wrong please, I'm a bit confused since interpro_ac is
> part from Core ProteinFeature.  (EnsEMBL::ProteinFeature::interpro_ac)
>
> Best regards,
> Guillermo.
>
>
> On 05/09/2013 04:16 PM, Guillermo Marco Puche wrote:
>
> Hello,
>
> Does anyone coded a plugin to obtain InterPro ID and description for VEP?
> I've looked in VEP repo without luck.
>
> I want to know before start coding.
>
> Thank you !
>
> Best regards,
> Guillermo.
>
>
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> --
>  ------------------------------
>
> Guillermo Marco Puche
>
> Bioinformatician, Computer Science Engineer.
> Sistemas Genómicos S.L.
> Phone: +34 902 364 669
> Fax: +34 902 364 670
> www.sistemasgenomicos.com
>
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