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

[Fiona Cunningham]

 Dear Alison,

Thank you for your comments. As Ewan says, we will be integrating
further analysis into our variant pipeline and this will also extend
to saying whether a variant is in a highly conserved area (based on
GERP scores). This functionality can be extended to the API script
although it is harder to do on the website as these analyses will take
longer.

Fiona

------------------------------------------------------
Fiona Cunningham
Ensembl Variation Project Leader, EBI
www.ensembl.org
www.lrg-sequence.org
t: 01223 494612 || e: fiona at ebi.ac.uk



On 18 November 2010 10:36, Alison Meynert <alison.meynert at hgu.mrc.ac.uk> wrote:
>> 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
>>>>
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>>>
>>>
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>>
>
> --
> Alison Meynert
> MRC Human Genetics Unit, Edinburgh
> alison.meynert at hgu.mrc.ac.uk
>
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