Question: Synonymous Mutations And Their Effect On Splice Site.
1
gravatar for Omid
7.8 years ago by
Omid560
Netherlands
Omid560 wrote:

Hi To analysis exome sequence data sometimes people exclude synonymous mutation.BUT it might affect on splice sites depend on how far it is from splice sites.

I have a list of synonymous variants.What is the easiest way to analyze these kind of mutations.I mean an on line web page where I upload my variants list and have a batch output.Thanks

exome • 2.7k views
ADD COMMENTlink written 7.8 years ago by Omid560

Hi. How did you call these synonymous variants? If you used PolyPhen etc., I think it would have told you if the mutation is splice site mutation.

ADD REPLYlink written 7.8 years ago by Vikas Bansal2.4k
1
gravatar for ff.cc.cc
7.8 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

"Ensembl provides the facility to predict the functional consequences of known and unknown variants using the Variant Effect Predictor (VEP)"

Try VEP here.

ADD COMMENTlink written 7.8 years ago by ff.cc.cc1.3k

Thanks.I tried VEP for 44 synonymous variants but that sounds in these variants we do not have SIFT or PolyPhen prediction in VEP.

ADD REPLYlink written 7.8 years ago by Omid560
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