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

[Ewan Birney]

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
>>
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>
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