Question: How can I know if snp is inside a protein domain?
1
gravatar for iraun
5.6 years ago by
iraun3.7k
Norway
iraun3.7k wrote:

I've some snps covering my gene X. I want to know if any of those snps is included in a domain of the protein encoded by my gene X. Anyone can suggest me how can I know the coordinates of the domains of my gene to see if my snps are included in these regions? Or any other method to know this?

Thanks in advance,
 

snp protein domain • 1.6k views
ADD COMMENTlink modified 5.6 years ago by Pierre Lindenbaum128k • written 5.6 years ago by iraun3.7k
3
gravatar for Pierre Lindenbaum
5.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

VEP ( http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html ) has got an option '--domains'

--domains          Adds names of overlapping protein domains to output. Not used by default
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Pierre Lindenbaum128k

Thanks Pierre, this is exactly what I was looking for.

ADD REPLYlink written 5.6 years ago by iraun3.7k

Pierre, you could write a nice paper on the nsSNP frequency and VEP scores across different InterPro domains/familes

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by cdsouthan1.8k
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