How Do Variable Substitution Rates Influence Ka and Ks Calculations?
The ratio of nonsynonymous substitution rate(Ka)to synonymous substitution rate(Ks)is widely used as an indicator of selective pressure at sequence level among different species, and diverse mutation models have been incorporated into several computing methods. We have previously developed a new γ/-MYN method by capturing a key dynamic evolution trait of DNA nucleotide sequences, in consideration of varying mutation rates across sites. We now report a further improvement of NG, LWL, MLWL, LPB, MLPB, and YN methods based on an introduction of gamma distribution to illustrate the variation of raw mutation rate over sites. The novelty comes in two ways:(1)we incorporate an optimal gamma distribution shape parameter a into γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, and γ-YN methods;(2)we investigate how variable substitution rates affect the meth-ods that adopt different models as well as the interplay among four evolutional features with respect to Ka/Ks computations. Our results suggest that variable substitution rates over sites under negative selection exhibit an opposite effect on ω estimates compared with those under positive selection. We believe that the sen-sitivity of our new methods has been improved than that of their original methods under diverse conditions and it is advantageous to introduce novel parameters for Ka/Ks computation.
作 者： Dapeng Wang Song Zhang Fuhong He Jiang Zhu Songnian Hu Jun Yu 作者单位： Dapeng Wang,Fuhong He,Jiang Zhu(CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China;Graduate University of Chinese Academy of Sciences, Beijing 100049, China)Song Zhang(CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China;Graduate University of Chinese Academy of Sciences, Beijing 100049, China;Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China)
Songnian Hu(CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China)
Jun Yu(CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China;Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China)
刊 名： 基因组蛋白质组与生物信息学报（英文版） 英文刊名： GENOMICS、PROTEOMICS & BIOINFORMATICS 年，卷(期)： 2009 7(3) 分类号： Q5 关键词： substitution rate approximate method gamma distribution Ka Ks