基于DNA序列K-tuple分布的一种非序列比对分析  

A new alignment-free sequence analysis based on the distribution of K-tuple

作　　者：沈娟[1] 吴文武[2] 解小莉[1] 郭满才[1] 袁志发[1] 

机构地区：[1]西北农林科技大学理学院,杨凌712100 [2]西北农林科技大学生命科学学院,杨凌712100

出　　处：《遗传》2010年第6期606-612,共7页Hereditas（Beijing)

基　　金：回国人员科研启动项目(编号:Z111020834)资助

摘　　要：文章在基因组K-tuple分布的基础上,给出了一种推测生物序列差异大小的非序列比对方法。该方法可用于衡量真实DNA序列和随机重排序列在K-tuple分布上的差异。将此方法用于构建含有26种胎盘哺乳动物线粒体全基因组的系统树时,随着K的增大,系统树的分类效果与生物学一致公认的结果愈加匹配。结果表明,用此方法构建的系统进化树比用其他非序列比对分析方法构建的更加合理。Based on the distribution of K-tuple in complete genome, a method without doing sequence alignment to infer difference of biological sequence is proposed in this paper. The method can be used to measure the difference of distribution on K-tuple between the native DNA sequences and the corresponding randomized ones. Applied to construct phylogenetic trees of the complete mitochondrial genomes of 26 species of placental mammals, with K increasing, it yields phylogenetic trees of which the classification effect increasingly matches the result widely recognised by the biological field. The final results show that the phylogenetic trees built by this method is more reasonable than by other alignment-free sequence methods.

关 键 词：K-tuple 非序列比对 DNA序列 线粒体全基因组 系统树 

分 类 号：Q78[生物学—分子生物学]