Computing Ka and Ks with a consideration of unequal transitional substitutions

doi:10.1186/1471-2148-6-44

	Computing Ka and Ks with a consideration of unequal transitional substitutions
	Zhang, Zhang ; Li, Jun ; Yu, Jun
	2006-06-02
发表期刊	BMC EVOLUTIONARY BIOLOGY
ISSN	1471-2148
卷号	6 页码:10
摘要	Background: Approximate methods for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) among protein-coding sequences have adopted different mutation (substitution) models. In the past two decades, several methods have been proposed but they have not considered unequal transitional substitutions (between the two purines, A and G, or the two pyrimidines, T and C) that become apparent when sequences data to be compared are vast and significantly diverged. Results: We propose a new method (MYN), a modified version of the Yang-Nielsen algorithm (YN), for evolutionary analysis of protein-coding sequences in general. MYN adopts the Tamura-Nei Model that considers the difference among rates of transitional and transversional substitutions as well as factors in codon frequency bias. We evaluate the performance of MYN by comparing to other methods, especially to YN, and to show that MYN has minimal deviations when parameters vary within normal ranges defined by empirical data. Conclusion: Our comparative results deriving from consistency analysis, computer simulations and authentic datasets, indicate that ignoring unequal transitional rates may lead to serious biases and that MYN performs well in most of the tested cases. These results also suggest that acquisitions of reliable synonymous and nonsynonymous substitution rates primarily depend on less biased estimates of transition/transversion rate ratio.
DOI	10.1186/1471-2148-6-44
收录类别	SCI
语种	英语
WOS研究方向	Evolutionary Biology ; Genetics & Heredity
WOS类目	Evolutionary Biology ; Genetics & Heredity
WOS记录号	WOS:000240066500001
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：61[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/2XEOYT63/10559
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, Inst Comp Technol, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Beijing Genom Inst, Beijing 101300, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 4.Zhejiang Univ, James D Watson Inst Genome Sci, Hangzhou Genom Inst, Key Lab Genom Bioinformat Zhejiang Prov, Hangzhou 310027, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Zhang,Li, Jun,Yu, Jun. Computing Ka and Ks with a consideration of unequal transitional substitutions[J]. BMC EVOLUTIONARY BIOLOGY,2006,6:10.
APA	Zhang, Zhang,Li, Jun,&Yu, Jun.(2006).Computing Ka and Ks with a consideration of unequal transitional substitutions.BMC EVOLUTIONARY BIOLOGY,6,10.
MLA	Zhang, Zhang,et al."Computing Ka and Ks with a consideration of unequal transitional substitutions".BMC EVOLUTIONARY BIOLOGY 6(2006):10.