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  1. Jalview
  2. JAL-1681

Codon consensus on protein view linked to cDNA alignment

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.9
    • Component/s: analysis
    • Labels:
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      Description

      It would be good to be able to show the nucleotide alignment's average consensus for each codon as an annotation row on the protein alignment. This is somewhat like what is done in genome viewers showing conservation across model organisms for a particular protein coding region, but also allows someone to see places where there is purifying selection.

      In fact, the difference between the nucleotide variation and amino acid variation is effectively a measure of the rate of synonymous to non-synonymous mutation (but we'll not go there for now!).

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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