目的基于柯萨奇病毒A组6型(coxsackievirus group A type 6,CV-A6)VP1编码区寻找与其流行强度增加有关的关键氨基酸位点。方法对GenBank数据库中全部CV-A6 VP1编码区核苷酸序列进行筛选,获得其中的1533条序列进行比对。使用RAxML软件构...目的基于柯萨奇病毒A组6型(coxsackievirus group A type 6,CV-A6)VP1编码区寻找与其流行强度增加有关的关键氨基酸位点。方法对GenBank数据库中全部CV-A6 VP1编码区核苷酸序列进行筛选,获得其中的1533条序列进行比对。使用RAxML软件构建最大似然树。使用Shannon Entropy在线分析工具计算序列的氨基酸置换熵值,并用Datamonkey在线分析平台通过MEME,SLAC和FUBAR三种方法来分析正向选择位点。结果目前全球流行的CV-A6以D3基因亚型为主。在VP1编码区存在三个高度可变的氨基酸位点,分别是VP1-5、VP1-30、VP1-137。三种方法均发现VP1-5、VP1-90、VP1-137三个位点在流行中受到过正向选择的作用。结论应继续加强对D3基因亚型CV-A6的监测,D3基因亚型的CV-A6在位于DE环中的VP1-137高度可变且受到了正向选择的作用,需要加以重视,并通过进一步研究来确定它与D3亚型广泛流行的关系。展开更多
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 mode...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.展开更多
文摘目的基于柯萨奇病毒A组6型(coxsackievirus group A type 6,CV-A6)VP1编码区寻找与其流行强度增加有关的关键氨基酸位点。方法对GenBank数据库中全部CV-A6 VP1编码区核苷酸序列进行筛选,获得其中的1533条序列进行比对。使用RAxML软件构建最大似然树。使用Shannon Entropy在线分析工具计算序列的氨基酸置换熵值,并用Datamonkey在线分析平台通过MEME,SLAC和FUBAR三种方法来分析正向选择位点。结果目前全球流行的CV-A6以D3基因亚型为主。在VP1编码区存在三个高度可变的氨基酸位点,分别是VP1-5、VP1-30、VP1-137。三种方法均发现VP1-5、VP1-90、VP1-137三个位点在流行中受到过正向选择的作用。结论应继续加强对D3基因亚型CV-A6的监测,D3基因亚型的CV-A6在位于DE环中的VP1-137高度可变且受到了正向选择的作用,需要加以重视,并通过进一步研究来确定它与D3亚型广泛流行的关系。
文摘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.
