Question: How to find the amino acid codons corresponding to a subset of a range of genomic positions
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gravatar for madsheilskov
3.9 years ago by
Denmark
madsheilskov0 wrote:

 

Recently I asked how one - if given some genomic positions as a GRanges object - could find the amino acid codons that corresponded to these positions (if in a coding exon): C: How to find the amino acid codon corresponding to a translated genomic position . Got a nice solution from the site.

I now find myself in a similar but somewhat extended (complicated ?) situation. I have a GRanges with ~1000 > width > 330  bases. Parts of these ranges overlap with coding exons and I wish to know what are the corresponding amino acid sequences in these overlaps. The catch is that part of each range - since they are genomic - may also overlap with intron or untranslated parts of exons before they 'continue' into some translated part. tried to fiddle around the solution I got in the answer to the above question/link, but couldnt figure it out. How can I find the amino acids "overlapping" these ranges ?

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