This MedLibrary.org supplementary page on Ka/Ks ratio is provided directly from the open source Wikipedia as a service to our readers. Please see the note below on authorship of this content, as well as the Wikipedia usage guidelines. To search for other content from our encyclopedia supplement, please use the form below:
Related Sponsors
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.
|
|||||||||||
 |
This genetics article is a stub. You can help Wikipedia by expanding it. |
Wikipedia content modification information:
- This page was last modified on 25 September 2008, at 19:52.
Wikipedia Authorship and Review
Wikipedia content provided here is not reviewed directly by MedLibrary.org. Wikipedia content is authored by an open community of volunteers and is not produced by or in any way affiliated with MedLibrary.org.
Wikipedia Usage Guidelines
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article on "Ka/Ks ratio".
The URL for this specific entry is:
All Wikipedia text is available under the terms of the GNU Free Documentation License. (See Copyrights for details). Wikipedia® is a registered trademark of the Wikimedia Foundation, Inc.