How to find the amino acid codons corresponding to a subset of a range of genomic positions
0
0
Entering edit mode
madsheilskov ▴ 10
@madsheilskov-9317
Last seen 4.2 years ago
Denmark

 

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 ?

genomicfeatures genomicranges cds overlap • 1.5k views
ADD COMMENT

Login before adding your answer.

Traffic: 800 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6