[ensembl-dev] post-translational modifications and the snp effect predictor

Alison Meynert alison.meynert at hgu.mrc.ac.uk
Thu Nov 18 10:36:12 GMT 2010


 > That said, I think this would be an excellent project; Alison, you could
 > do a geek-for-a-week
 > program to pilot this perhaps and explore what was possible/sensible?

Good to know there are more features in the pipeline; I'd also like to 
see GERP scores as an option.

Post-translational modifications are not a high priority for me, so I 
will have to say no for now, but perhaps someone else on the list would 
be interested.

Cheers,
Alison

On 17/11/2010 15:22, Ewan Birney wrote:
>
> This I think drifts towards further integration with Uniprot Features
> coming down
> into the Ensembl Peptide space to allow for this to occur. I think this
> would be a great
> thing...
>
>
> ... However, I think earlier priorities in the Variant predictor team
> are (Fiona to correct
> me if wrong) :
>
> Integrating a classical amino acid change model (SIFT, PolyPhen)
>
> Doing SNPs in non coding regions, in particular those in chip-seq peaks
> and ones
> which changes motifs found in their cognate chip-seq peaks.
>
>
>
> That said, I think this would be an excellent project; Alison, you could
> do a geek-for-a-week
> program to pilot this perhaps and explore what was possible/sensible?
>
>
>
> On 17 Nov 2010, at 13:59, Graham Ritchie wrote:
>
>> Hi Alison,
>>
>> We don't have any immediate plans to consider the effect of variations
>> on post-translational modification, but we are currently working on
>> extending and improving our variation consequence system and this is
>> certainly something we will think about. We don't think that data
>> about PTM is included anywhere in Ensembl, do you know of a source for
>> this sort of data that we could potentially import from?
>>
>> Cheers,
>>
>> Graham
>>
>> Ensembl variation
>>
>>
>> On 17 Nov 2010, at 12:16, Alison Meynert wrote:
>>
>>> The SNP effect predictor Perl script is excellent - thanks for making
>>> that available. Are there plans to include a consequence type for
>>> variations that change sites of post-translational modification? I'm
>>> not even sure if Ensembl stores these, but have been getting some
>>> questions from biologists about this type of variant as a possible
>>> disease cause.
>>>
>>> Cheers,
>>> Alison
>>>
>>> --
>>> Alison Meynert
>>> MRC Human Genetics Unit, Edinburgh
>>> alison.meynert at hgu.mrc.ac.uk
>>>
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>
>>
>> _______________________________________________
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>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>

-- 
Alison Meynert
MRC Human Genetics Unit, Edinburgh
alison.meynert at hgu.mrc.ac.uk




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