Question: Mapping genomic coordinates to protein-relative coordinates
0
gravatar for Shixiang
2.7 years ago by
Shixiang70
Shanghai
Shixiang70 wrote:

How to translate mutations in genome/exome to string of amino acid, with amino acid resulting from the mutation centrally situated.

snp rna-seq sequence R gene • 912 views
ADD COMMENTlink modified 2.7 years ago by arta610 • written 2.7 years ago by Shixiang70
1
gravatar for arta
2.7 years ago by
arta610
Sweden
arta610 wrote:

You are looking for six frame translation and you can use translate function in R. Here you can find example.

ADD COMMENTlink written 2.7 years ago by arta610
1

I am going to guess that OP is looking for something more specific. Like Ve!P/snpEff but with more sequence padded to both sides of changed AA (which both will show).

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax92k

The function can translate DNA to Protein sequence, but I am looking for a translation which will think about the location of DNA sequence.

ADD REPLYlink written 2.7 years ago by Shixiang70

Not exactly sure what you are saying here. Are you referring to frame of translation?

ADD REPLYlink written 2.7 years ago by genomax92k

like this function, but I want to find hg38 other than ensembl version annotation.

ADD REPLYlink written 2.7 years ago by Shixiang70
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