[ensembl-dev] determining non-synonymous variants

[Ryan Giuliany]

Perfect, thanks!

From: Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Thu, 8 Mar 2012 09:59:35 -0800
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] determining non-synonymous variants

Hi Ryan

You can use Ensembl's Variant Effect Predictor (VEP). See the following URL for details:

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

Cheers

Will McLaren
Ensembl Variation

On Thursday, 8 March 2012, Ryan Giuliany <rgiuliany at bccrc.ca<mailto:rgiuliany at bccrc.ca>> wrote:
> Hi,
>
> I need to be able to determine, for a list of chromosomal positions, if each will result in amino acid substitution or not.
>
> I've searched around online and gone through the perl API's but I'm not seeing an overly straightforward way of achieving this.  For example, I could possibly do it by retrieving the overlapping transcript, copying it, modifying the base in question, translating both the original and the copy and comparing the peptides, but this seems…unnecessarily complex.
>
> Is there an easy way that I've missed?
>
> Thanks!!
> Ryan
>
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