[ensembl-dev] transcript variation effect

[Graham Ritchie]

Hi Duarte,

There isn't a straightforward way to do this in the API at the moment, we may add support for this at some point. The way we do this in the variation consequence pipeline is essentially to splice the variant sequence into the CDS of the transcript and then translate the resulting mutated sequence, but there are a few gotchas along the way! I attach a file which includes a subroutine mutate_transcript which takes this approach and returns the mutated peptide sequence of a transcript, given a Transcript object and a VariationFeature object. There's a little bit of test code around it showing how to call it, so you should be able to run the script - hopefully it makes sense and you can adapt it to your requirements. There isn't a lot of error checking, and I have only briefly tested it so please check the results make sense!

Let me know if you have any questions about it.

Cheers,

Graham

Ensembl variation

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On 1 Feb 2011, at 16:38, Duarte Molha wrote:

> Hello
> 
> I apologize if this is a newbie question but I have been working on a script that calculates the consequences of a variation on each possible transcript within a gene.
> It works fine and I am able to get all possible consequences. Nevertheless I am finding it hard to to find a way to calculate the new protein sequence that results form say a non-synonymous coding variation.
> I am able to retrieve the translation of the transcript I am interested in but I did not find a way to get the resulting protein sequence from the variation I am interested in.
> 
> Would anybody be able to point me in the right direction?
> 
> Thank you for your help
> 
> Best regards
> 
>    Duarte Molha
> 
> =========================
>      Duarte Miguel Paulo Molha
>   Email: duartemolha at gmail.com
> =========================
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