Question: Mapping genomic coordinates to protein-relative coordinates
0
gravatar for Shixiang
21 months ago by
Shixiang50
Shanghai
Shixiang50 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 • 689 views
ADD COMMENTlink modified 21 months ago by arta540 • written 21 months ago by Shixiang50
1
gravatar for arta
21 months ago by
arta540
Sweden
arta540 wrote:

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

ADD COMMENTlink written 21 months ago by arta540
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 21 months ago • written 21 months ago by genomax75k

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 21 months ago by Shixiang50

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

ADD REPLYlink written 21 months ago by genomax75k

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

ADD REPLYlink written 21 months ago by Shixiang50
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