[BioC] Distinguish Synonymous vs. Non-synonymous SNPs

Michael Dondrup Michael.Dondrup at uni.no
Fri Jan 29 12:10:44 CET 2010

Hi Xiwei,
do you mean SNPs that result in non-synonymous vs  synonymous coding? Then a biomart query might do the 
job and therefore the package biomaRt could be used to query from within R.  There is a filter in biomart for different 
consequence types of SNPs, one of which is NON_SYNONYMOUS_CODING. You can check which filter seems appropriate
This lengthy Url represents a possible query in the biomart web interface:


it should be possible to set identical parameters in the bioconductor package biomaRt although I didn't try this yet.


Am Jan 29, 2010 um 1:57 AM schrieb Wu, Xiwei:

> Dear list, 
> I have a list of SNPs with chromosome location, and trying to see which
> ones are non-synonymous. Are there any packages/functions that can
> distinguish synonymous and non-synonymous SNPs? I tried to search the
> list, but could not find anything related. Thanks in advance.
> Xiwei
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