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组分矢量方法与小亚基核糖体RNA方法构建进化树的对比

发表时间:2011-03-15  浏览量:1864  下载量:842
全部作者: 叶远浓,郭锋彪
作者单位: 电子科技大学生命科学与技术学院
摘 要: 采用基于小亚基核糖体RNA(16S rRNA)序列和组分矢量(composition vector)两种方法构建进化树。在高层分支(界)上,用两种方法对115个物种做进化树分析,在组分矢量方法中,当短串长度K值为6和5时,能很好地把三界的物种分开,与基于16S rRNA方法构建的进化树大致相同;在底层分支上,组分矢量方法不如基于16S rRNA方法构建的进化树好。再单独对低层分支(种)进行分析,选取E.coli的27个株,发现组分矢量方法在K=4时,分类效果最好,优于基于16S rRNA方法构建的进化树。
关 键 词: 生物物理学;进化树;小亚基核糖体 RNA;16S rRNA;组分矢量方法;CVTree
Title: Comparison of two methods in constructing phylogenetictree: the composition vector approach and the method based on the small subunit ribosomal RNA
Author: YE Yuannong, GUO Fengbiao
Organization: School of Life Science and Technology, University of Electronic Science and Technology of China
Abstract: In this paper, two methods, one based on small subunit ribosomal RNA (16S rRNA) sequence and the other on composition vector, were adopted for constructing phylogenetic trees. In the top branch (kingdom), phylogenetic analysis for 115 species showed that three kingdoms were separated properly by composition vector when K-string length equaled 5 or 6, as well as by 16S rRNA sequence. However, the composition vector approach was not so good as the other on the lower branch. Further more, 27 strains of Escherichia coli were selected for a more detailed lower branches (species) analysis and found that the composition vector approach (best classification achieved when K=4) was better than the method based on 16S rRNA.
Key words: biophysics; phylogenetic tree; small subunit ribosomal RNA; 16S rRNA; composition vector approach; CVTree
发表期数: 2011年3月第5期
引用格式: 叶远浓,郭锋彪. 组分矢量方法与小亚基核糖体RNA方法构建进化树的对比[J]. 中国科技论文在线精品论文,2011,4(5):427-434.
 
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