10 - cmb-2012, Vol. 1, No. 2页

计算分子生物学(网络版), 2012 年, 第 1 卷, 第 2 篇, 第 7-1 5 页
Jisuan Fenzi Shengwuxue (Online), 2012, Vol.1, No.2, 7-15
http://cmb.5th.sophiapublisher.com
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两个物种基因组寡聚核苷酸转移概率矩阵的
欧几里徳距离计算公式：


 
N
j i
j i j i y x D
1 ,
2
, , ) ( (3)
其中，N 为转移概率矩阵的总行数或总列数；
xi, j、yi, j 分别代表两个物种的转移概率矩阵中第 i 行第
j 列的元素值。
图 5 酿脓链球菌种内的 5 个菌株的系统发育树
注: A: 基于 16S rRNA 的核苷酸序列构建的系统发育树 ; B:
基于基因组三核苷酸转移概率矩阵的联合直方图散度构建
的系统发育树
Figure 5 The phylogeny tree of 5 strains of Streptococcus pyogenes.
Note: A: The phylogeny tree based on 16S rRNA gene
constructed by neighbor-joint method; B: The phylogeny tree
based on joint histogram divergence of genomic trinucleotide
transition probability matrix
另外，基于单基因的系统发育分析方法存在着
局限性且分辨力有限，它只对种以上的分类单元具
有较高的分辨力，而对种以下亲缘关系十分接近的
物种则难以区分(Bohlin et al., 2008)。对于用单基因
序列比对无法区分的物种，我们用联合直方图散度
进行聚类分析，由此评估联合直方图散度在系统发
育分析方面的优势。这里，我们先用 CLUSTAL X
对 11 个物种的 16S rRNA 基因进行多重序列比对，
接着用邻接法构建单基因系统发育树；同时，通过
构建这些物种的联合直方图散度矩阵，并利用
PHYLIP 软件进行聚类，推断它们的系统发育关系；
最后，通过比较上述两种手段构建的系统发育树，
对新方法进行评估。
作者贡献
严翠婷是研究的主要执行人，包括数据采集、分析和初稿写
作；黄庆生编写程序，参与部分数据分析和讨论；章芬参与
部分数据分析；方颖是项目负责人，指导整个实验设计、数
据分析、论文写作和修改。
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