How Do Variable Substitution Rates Influence Ka and Ks Calculations?

查看全文 作　　者：Dapeng [1,2]Wang;Song [1,2,3]Zhang;Fuhong [1,2]He;Jiang [1,2]Zhu;Songnian [1]Hu;Jun [1,3]Yu

机构地区：[1]CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China;[2]Graduate University of Chinese Academy of Sciences, Beijing 100049, China;[3]Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China

出　　处：《Genomics, Proteomics & Bioinformatics》索引2009年第7卷第3期,共12页

基　　金：supported by the National Basic Research Program of China (Grant No. 2006CB910404) awarded to JY 摘　　要：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 methods 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 sensitivity 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. 关键词：计算方法变量代换液体聚丁二烯演化特征变量替换核苷酸序列压力水平序列选择

相关文献

参考文献（37）
引证文献（4）
耦合文献（108）

参考文献(37)

引证文献(4)

耦合文献(108)

互联网出版许可证新出网证(渝)字10号全国400电话 - 免长途话费

How Do Variable Substitution Rates Influence Ka and Ks Calculations?

参考文献(37)

引证文献(4)

耦合文献(108)

用户提示