[ensembl-dev] VEP Grantham amino acid distance

[Duarte Molha]

Hi Guillermo

I am not part of the ensemble Dev team... but I have already implemented a plugin that retrieves Grantham scores. I based it on the Blosum62 plugin... but basically gave it a different scoring matrix taken from the same paper as Chris referenced.

I hope it is useful to you..

Best regards

Duarte


From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Guillermo Marco Puche
Sent: 29 April 2013 09:05
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP Grantham amino acid distance

Hello Chris,

As I said I'm implementing this as an Ensembl Variant Effect Predictor plugin.
Input is an VCF file.

Best regards,
Guillermo.

On 04/29/13 10:03, cj5 at sanger.ac.uk<mailto:cj5 at sanger.ac.uk> wrote:

Hi Guillermo,

Not sure of your requrements, but if you want a simple lookup of a mtrix based upon the original paper,



Grantham, R. Amino Acid Difference Formula to Help Explain Protein Evolution, Science 1974 Sep 6;185(4154):862-4.



please see attached.



regards

Chris Joyce



Hello,



I'm trying to calculate Grantham AA distance as a VEP plugin.



Currently I'm doing it parsing HGSVp and calculating distance between

the two AA being parsed.



Do you guys believe there's an easier and more efficient way to do this?



Thank you.



Best regards,

Guillermo.

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