同源DNA序列中间隔位点的核苷酸最近邻插补  

Nucleotide nearest neighbor interpolation for gap sites in homologous DNA sequences

作　　者：秦雪瑞 刘雄恩[1] QIN Xuerui;LIU Xiongen(College of Computer and Information Science,Fujian Agriculture and Forestry University,Fuzhou,Fujian 350002,China)

机构地区：[1]福建农林大学计算机与信息学院,福建福州350002

出　　处：《福建农林大学学报（自然科学版）》2018年第5期633-640,共8页Journal of Fujian Agriculture and Forestry University:Natural Science Edition

基　　金：福建农林大学2016年度科技创新专项基金项目(CXZX2016027)

摘　　要：针对分子系统发育重建时忽略同源DNA序列中的间隔位点导致进化信息丢失和序列间进化距离偏低估计的问题,基于最小进化原理并借鉴统计学中缺失数据处理的方法,提出核苷酸最近邻插补间隔位点,对插补后序列再运用4-状态DNA进化马尔可夫模型估算序列间进化距离的方法.对3组同源DNA序列在不同方法下进行距离估算的对照测试,结果表明:5-状态的F81+gap和F84+gap模型不能有效融合间隔所携带的indel信息,反而更加低估序列间距离;改进的同类模型F81+gap'则在一定程度上降低了距离的偏低估计,而核苷酸最近邻插补处理方法可以融合DNA突变中更多的indel信息.-In molecular phylogenetic reconstruction,ignoring gap site in homologous DNA sequences may lose evolutionary information and cause underestimation of evolutionary distances between sequences.To solve this problem,nucleotide nearest neighbor interpolation for gap sites was proposed.Different from Markov models for DNA evolutionary-process which see gap as the 5th state,nearest neighbor interpolation is based on the principle of minimum-evolution and referenced processing method for missing data in statistics.Subsequently,4-state Markov models is used in distance estimation for homologous DNA sequences after the interpolation.Last,tests of distance estimation on 3 groups of homologous DNA sequences under different methods were made.Results showed that 5-state models such as F81+gap and F84+gap,can not integrate indel information carried by gap sites effectively and lead to more undervalued distances between sequences.The improved similar model F81+gapr can reduce underestimation of distance to some certain extent,and the nucleotide nearest neighbor interpolation processing method can integrate more indel information in DNA mutations.

关 键 词：同源DNA序列 间隔 插入/缺失 缺失数据 进化距离 最近邻插补 

分 类 号：O211.62[理学—概率论与数理统计] O241.6[理学—数学]