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Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach
Qi, J; Wang, B; Hao, BI; Qi, J , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
2004
发表期刊JOURNAL OF MOLECULAR EVOLUTION
ISSN0022-2844
卷号58期号:1页码:1-11
摘要A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The only "parameter" in the method is the length K of the oligopeptides, which serves to tune the "resolution power" of the method. The topology of the trees converges with K increasing. Applied to a total of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, it yields an unrooted tree that agrees with the biologists' "tree of life" based on SSU rRNA comparison in a majority of basic branchings, and especially, in all lower taxa.
部门归属Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China; Fudan Univ, T Life Res Ctr, Shanghai 200433, Peoples R China
关键词Universal Tree Life Archaeal
学科领域Physics
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收录类别SCI
WOS记录号WOS:000188112200001
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被引频次:232[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/14146
专题1978-2010年知识产出
通讯作者Qi, J , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
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Qi, J,Wang, B,Hao, BI,et al. Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach[J]. JOURNAL OF MOLECULAR EVOLUTION,2004,58(1):1-11.
APA Qi, J,Wang, B,Hao, BI,&Qi, J , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China..(2004).Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach.JOURNAL OF MOLECULAR EVOLUTION,58(1),1-11.
MLA Qi, J,et al."Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach".JOURNAL OF MOLECULAR EVOLUTION 58.1(2004):1-11.
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