Question: convert SNP calls to amino acid change
0
gravatar for tangming2005
2.2 years ago by
tangming20052.2k
Houston/MD Anderson Cancer Center
tangming20052.2k wrote:

I am wondering if I have a maf file describing the snps, how can I easily convert it to amino acid changes.

 " Missense_Mutation    23    66937331    66937331    T    A" ---------->  L729I  

I know I can grab the sequences around the mutation point (also needs to know where is the start codon),

and use the triplets table to find it out the changes.

I just want to know if there is an existing tool for that.

Thanks,

Ming 

 

 

snp amino acid • 1.2k views
ADD COMMENTlink modified 2.2 years ago by cpad01123.8k • written 2.2 years ago by tangming20052.2k
4
gravatar for cpad0112
2.2 years ago by
cpad01123.8k
cpad01123.8k wrote:

Round about way is to

ADD COMMENTlink written 2.2 years ago by cpad01123.8k

Thanks for the link!

ADD REPLYlink written 2.2 years ago by tangming20052.2k
1
gravatar for tangming2005
2.2 years ago by
tangming20052.2k
Houston/MD Anderson Cancer Center
tangming20052.2k wrote:

It looks like VEP can do this job... http://useast.ensembl.org/info/docs/tools/vep/vep_formats.html?redirect=no

Ming

ADD COMMENTlink written 2.2 years ago by tangming20052.2k
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