| Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes |
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| 作者姓名： | ZHANG Wenjuan ZHANG Yuan ZHONG Yang |
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| 作者单位： | [1]School of Life Sciences, Fudan University, Shanghai 200433, China [2]Shanghai Center for Bioinformation Technology, Shanghai 201203, China |
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| 基金项目： | Acknowledgements The authors would like to thank the Bioinformatics Working Group in School of Life Sciences at Fudan University, and Masami Hasegawa and Ying Cao in the Institute of Statistical Mathematics （Tokyo） for helpful discussions. This work was supported by the National Basic Research Programs （973） （Grant Nos. 2002CB512801 ＆ 2003CB715904）, and New Century Excellent Talents in University Program. |
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| 摘 要： | The basic process of adaptive evolution by natural selection is the replacement of one allele gene by an- other with a higher fitness in a population. Detecting the adaptive evolution would be helpful for better un- derstanding of bio-evolutionary mechani…
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| 关 键 词： | 适应进化 阳性选择 氨基酸 肝炎病毒 包膜蛋白 HCV |
| 收稿时间： | 2006-01-25 |
| 修稿时间： | 2006-01-252006-07-12 |
Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes |
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| ZHANG Wenjuan ZHANG Yuan ZHONG Yang.Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes[J].Chinese Science Bulletin,2006,51(18):2236-2242. |
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| Authors: | Wenjuan Zhang Yuan Zhang Yang Zhong |
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| Institution: | (1) School of Life Sciences, Fudan University, Shanghai, 200433, China;(2) Shanghai Center for Bioinformation Technology, Shanghai, 201203, China |
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| Abstract: | Nonsynonymous-synonymous substitu- tion rate ratio (dN/dS) is an important measure for evaluating selective pressure based on the pro- tein-coding sequences. Maximum likelihood (ML) method with codon-substitution models is a powerful statistic tool for detecting amino acid sites under positive selection and adaptive evolution. We ana- lyzed the hepatitis C virus (HCV) envelope pro- tein-coding sequences from 18 general geno/ sub- types worldwide,and found 4 amino acid sites under positive selection. Since these sites are located in different immune epitopes,it is reasonable to antici- pate that our study would have potential values in biomedicine. It also suggests that the ML method is an effective way to detect adaptive evolution in virus proteins with relatively high genetic diversity. |
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| Keywords: | adaptive evolution positive selection amino acid sites hepatitis C virus envelope proteins |
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