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Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree
Qiu, Yu-Qing1; Tian, Xue2; Zhang, Shihua1
2015-09-01
发表期刊IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN1545-5963
卷号12期号:5页码:1112-1122
摘要Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes.
关键词Metagenomics abundance estimation taxonomy tree expectation-maximization algorithm
DOI10.1109/TCBB.2015.2415814
语种英语
资助项目National Natural Science Foundation of China[61379092] ; National Natural Science Foundation of China[61422309] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; Foundation for Members of Youth Innovation Promotion Association, CAS ; Outstanding Young Scientist Program of CAS ; Key Laboratory of Random Complex Structures and Data Science, CAS
WOS研究方向Biochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS类目Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS记录号WOS:000362909500014
出版者IEEE COMPUTER SOC
引用统计
文献类型期刊论文
条目标识符http://ir.amss.ac.cn/handle/2S8OKBNM/21018
专题应用数学研究所
通讯作者Qiu, Yu-Qing
作者单位1.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
2.Hangzhou Dianzi Univ, Sch Sci, Hangzhou 310018, Zhejiang, Peoples R China
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Qiu, Yu-Qing,Tian, Xue,Zhang, Shihua. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2015,12(5):1112-1122.
APA Qiu, Yu-Qing,Tian, Xue,&Zhang, Shihua.(2015).Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,12(5),1112-1122.
MLA Qiu, Yu-Qing,et al."Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 12.5(2015):1112-1122.
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