Ka/Ks ratio

Ka/Ks ratio

In genetics, the Ka/Ks ratio (or ω, dN/dS), is the ratio of the rate of non-synonymous substitutions (Ka) to the rate of synonymous substitutions (Ks), which can be used as an indicator of selective pressure acting on a protein-coding gene.

Methods for estimating Ka and Ks can be classified into two groups: approximate methods and maximum-likelihood methods. Approximate methods involve three basic steps: (1) counting the number of synonymous and nonsynonymous sites, (2) counting the number of synonymous and nonsynonymous substitutions, and (3) correcting for multiple substitutions. The maximum-likelihood approach uses the probability theory to finish all three steps in one go (Yang and Bielawski, 2000).

References

Li WH, Wu CI, Luo CC: A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 1985, 2(2):150-174.

Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3(5):418-426.

Li WH: Unbiased estimation of the Rates of synonymous and nonsynonymous substitution. J Mol Evol 1993, 36:96-99.

Pamilo P, Bianchi NO: Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 1993, 10(2):271-281.

Muse SV, Gaut BS: A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 1994, 11(5):715-724.

Goldman N, Yang Z: A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 1994, 11(5):725-736.

Comeron JM: A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J Mol Evol 1995, 41:1152-1159.

Ina Y: New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J Mol Evol 1995, 40:190-226.

Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 1997, 13:555-556.

Yang Z, Bielawski JP: Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution 2000, 15: 496-503.

Yang Z, Nielsen R: Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models. Mol Biol Evol 2000, 17(1):32-43.

Zhang Z, Li J, Yu J: Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC evolutionary biology 2006, 6:44.

Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J: KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics & Bioinformatics 2006, 4(4):259-263.


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