[BioC] Distinguish Synonymous vs. Non-synonymous SNPs
XWu at coh.org
Fri Jan 29 18:26:25 CET 2010
Thanks a lot for your help. I will give it a try. Is it good for novel
SNPs not in the dbSNP? The SNPs I got are from a sequencing project,
many of them are not in dbSNP.
From: Michael Dondrup [mailto:Michael.Dondrup at uni.no]
Sent: Friday, January 29, 2010 3:11 AM
To: Wu, Xiwei
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Distinguish Synonymous vs. Non-synonymous SNPs
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
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
> 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.
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