Question

Mapping genomic coordinates to protein-relative coordinates

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6.7 years ago

Shixiang ▴ 100

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

RNA-Seq R SNP sequence gene • 1.8k views

ADD COMMENT • link updated 6.7 years ago by arta ▴ 670 • written 6.7 years ago by Shixiang ▴ 100

score 1 · Answer 1 · 2018-03-22

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6.7 years ago

arta ▴ 670

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

ADD COMMENT • link 6.7 years ago by arta ▴ 670

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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 REPLY • link 6.7 years ago by GenoMax 147k

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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 REPLY • link 6.7 years ago by Shixiang ▴ 100

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

ADD REPLY • link 6.7 years ago by GenoMax 147k

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

ADD REPLY • link 6.7 years ago by Shixiang ▴ 100