Institute of Computing Technology, Chinese Academy IR
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 | |
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. |
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