Synonymous/Nonsynonymous Mutations (Ks/Ka)
Synonymous mutation rate (Ks) Mutations/substitutions of DNA base pairs that do not result in a change of amino acid sequence. Also known as a silent mutation.
Non-synonymous mutation rate (Ka) or (Kn) Mutations/substitutions of DNA base pairs that result in a single amino acid change on a given polypeptide. Also known as a substitution mutation.
Non-synonymous/Synonymous mutation ratio (Ka/Ks) Ratio of mutations that change a specific protein structure (non-synonymous, Ka) to mutations that do not change a specific protein. This ratio is used to estimate the selection pressure a given protein or section of DNA experiences. This ratio has been used in several ways: 1) to enhance gene predictions as areas of coding sequence will have a lower Ka/Ks ratio than non-coding areas; 2) determine differences in natural selection pressure on proteins.
- Neutral selection (Ka/Ks = 1) occurs when coding sequences
- Positive selection (Ka/Ks > 1)
- Purifying selection (Ka/Ks < 1)