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基因组时代的计算微生物学
Computational microbiology in genomic era

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文摘 微生物基因组和RNA序列构成生物学数据的重要部分.从基因组出发而且不用序列联配的CVTree和基于16S rRNA序列联配的LVTree,是两套原始数据和计算过程相互独立的构建原核生物亲缘树和分类系统的途径.这两套途径的自动化,使亲缘关系和分类系统成为大数据分析的副产品,可以帮助后继乏人的分类学摆脱困境.特别是基于基因组的CVTree,既提供了大范围研究的工具,又在种以下具有16S rRNA序列分析所不能企及的高分辨力,可以提出和解决一批新问题,开辟若干新方向.本文是相关研究工作的扼要综述.
其他语种文摘 Microbial genomes and RNA sequences comprise an important part of biological big data. CVTree is a whole-genome based and alignment-free method whereas LVTree is based on alignment of 16S rRNA sequences. They provide two independent ways to construct phylogenetic trees and to extract taxonomic information for prokaryotes. The automation of these two approaches make the study of prokaryotic phylogeny and classification by-product of big data analysis and come as a rescue to the declining discipline of taxonomy. Especially, the whole-genome based CVTree not only provides a tool for large-scale study but also possesses high resolution power at the species level and below, a distinctive feature beyond the reach of 16S rRNA sequence analysis. These methods taken together may open new directions in microbiological research. This paper is a brief review of our recent work.
来源 中国科学. 生命科学 ,2017,47(2):159-170 【核心库】
DOI 10.1360/N052016-00312
关键词 原核生物 ; 亲缘树 ; 分类系统 ; 不用序列联配的基因组比较 ; CVTree ; LVTree
地址

复旦大学物理系,理论生命科学研究中心, 上海, 200433

语种 中文
文献类型 研究性论文
ISSN 1674-7232
学科 生物工程学(生物技术)
基金 国家重大科学研究计划
文献收藏号 CSCD:5967429

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引证文献 1

1 肖静 古菌、生命树和真核细胞的功能演化 中国科学. 地球科学,2019,49(7):1082-1102
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