gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates

doi:10.1186/1745-6150-4-20

	gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
	Wang, Da-Peng 1,2; Wan, Hao-Lei 1,2; Zhang, Song 1,2,3; Yu, Jun 1,3
	2009-06-16
发表期刊	BIOLOGY DIRECT
ISSN	1745-6150
卷号	4 页码:18
摘要	Background: Over the past two decades, there have been several approximate methods that adopt different mutation models and used for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) based on protein-coding sequences across species or even different evolutionary lineages. Among them, MYN method (a Modified version of Yang-Nielsen method) considers three major dynamic features of evolving DNA sequences-bias in transition/transversion rate, nucleotide frequency, and unequal transitional substitution but leaves out another important feature: unequal substitution rates among different sites or nucleotide positions. Results: We incorporated a new feature for analyzing evolving DNA sequences-unequal substitution rates among different sites-into MYN method, and proposed a modified version, namely gamma(gamma)-MYN, based on an assumption that the evolutionary rate at each site follows a mode of gamma-distribution. We applied gamma-MYN to analyze the key estimator of selective pressure omega (Ka/Ks) and other relevant parameters in comparison to two other related methods, YN and MYN, and found that neglecting the variation of substitution rates among different sites may lead to biased estimations of omega. Our new method appears to have minimal deviations when relevant parameters vary within normal ranges defined by empirical data. Conclusion: Our results indicate that unequal substitution rates among different sites have variable influences on omega under different evolutionary rates while both transition/transversion rate ratio and unequal nucleotide frequencies affect Ka and Ks thus selective pressure omega. Reviewers: This paper was reviewed by Kateryna Makova, David A. Liberles (nominated by David H Ardell), Zhaolei Zhang (nominated by Mark Gerstein), and Shamil Sunyaev.
DOI	10.1186/1745-6150-4-20
收录类别	SCI
语种	英语
资助项目	National Basic Research Program of China[2006CB910404]
WOS研究方向	Life Sciences & Biomedicine - Other Topics
WOS类目	Biology
WOS记录号	WOS:000267521100001
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：108[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/11922
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Yu, Jun
作者单位	1.Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China
推荐引用方式 GB/T 7714	Wang, Da-Peng,Wan, Hao-Lei,Zhang, Song,et al. gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates[J]. BIOLOGY DIRECT,2009,4:18.
APA	Wang, Da-Peng,Wan, Hao-Lei,Zhang, Song,&Yu, Jun.(2009).gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.BIOLOGY DIRECT,4,18.
MLA	Wang, Da-Peng,et al."gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates".BIOLOGY DIRECT 4(2009):18.