[ensembl-dev] Question about variant effect predictor/Condel

[Graham Ritchie]

Hi Mark,

If you want to fetch all possible amino acid substitution predictions from sift or polyphen for a particular codon you could create an input file with every possible codon sequence at the position of interest, but it would be much more efficient to use the API to retrieve this set of substitution scores directly. We store all possible scores for every protein in the variation database as a matrix in a compressed form. The format is described in detail here:

http://www.ensembl.org/info/docs/variation/index.html#nsSNP_data_format

But the simplest way to access these matrices is to use an API script to fetch a ProteinFunctionPredictionMatrix for your protein of interest and then call its 'get_prediction' method to get the score for a particular position and amino acid, looping over all possible amino acids for your position. There is some detailed documentation on this class in the API documentation here:

http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1ProteinFunctionPredictionMatrix.html

You would need to work out which peptide position your codon maps to, but there are methods in the TranscriptVariationAllele class that should help you (probably translation_start and translation_end):

http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariation.html

We don't store a matrix for the condel scores because they are very quick to compute, given a sift and polyphen score, but you can compute this score using the get_condel_prediction subroutine in the Condel module.

http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1Condel.html

If you need any help gluing this all together let me know!

Cheers,

Graham


On 28 Nov 2011, at 15:53, Mark Aquino wrote:

> Hi,
> 
> I was wondering if it is possible to get functional predictions for entire codon swaps  (to easily get a score for any of the 19 non-reference AAs at any codon) using the variant effect predictor? My assumption, and through trying to insert a whole codon into a VCF and running VEP on that site, is that the answer is no but I wanted to double check, and perhaps see if it would be possible in the future or if it's simply unfeasible.
> 
> Best,
> Mark
> 
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