Question: Searching for mutation
0
gravatar for nesrine.trabelsi.n
10 weeks ago by
nesrine.trabelsi.n0 wrote:

Hello,

I have a gene and i want to get a list of all the mutations and variants that were described until now for this gene in cancer (or the proteine because i have some AA mutations for the proteine). I used cosmic but i want other tool or R package more reliable because i'll do the same work with other genes

Is there any tool or R package that allowed me to get the list of all the mutations for a gene rather then searching for it one by one with AA mutation positions?

Thank you

snp variant mutation R gene • 132 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by nesrine.trabelsi.n0

Hello,

what do you mean by "all the mutations"? You always need a database you can ask for this question.

If you are able to do some scripting maybe the ensembl REST-Api with its overlap endpoint is something for you. E.g. this give you all somatic variants listed in COSMIC for BRCA2:

http://rest.ensembl.org/overlap/id/ENSG00000139618?feature=somatic_variation;variant_set=ph_cosmic;content-type=application/json

fin swimmer

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by finswimmer6.2k

Hello, For Example, for IDH1, we found the mutations R132H or R132S and many other mutations... So i want a tool that give me the names of all the mutations of IDH1 (for example) and their positions or the variants that were described with their identifier

ADD REPLYlink written 10 weeks ago by nesrine.trabelsi.n0
ADD REPLYlink written 10 weeks ago by finswimmer6.2k
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