ITP OpenIR  > 理论物理所2014年知识产出
Self-organizing approach for meta-genomes
Zhu, JF; Zheng, WM; Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China.
2014
发表期刊COMPUTATIONAL BIOLOGY AND CHEMISTRY
ISSN1476-9271
卷号53期号:Part A页码:118-124
摘要We extend the self-organizing approach for annotation of a bacterial genome to analyze the raw sequencing data of the human gut metagenome without sequence assembling. The original approach divides the genomic sequence of a bacterium into non-overlapping segments of equal length and assigns to each segment one of seven 'phases', among which one is for the noncoding regions, three for the direct coding regions to indicate the three possible codon positions of the segment starting site, and three for the reverse coding regions. The noncoding phase and the six coding phases are described by two frequency tables of the 64 triplet types or 'codon usages'. A set of codon usages can be used to update the phase assignment and vice versa. An iteration after an initialization leads to a convergent phase assignment to give an annotation of the genome. In the extension of the approach to a metagenome, we consider a mixture model of a number of categories described by different codon usages. The Illumina Genome Analyzer sequencing data of the total DNA from faecal samples are then examined to understand the diversity of the human gut microbiome. (C) 2014 Elsevier Ltd. All rights reserved.
部门归属[Zhu, Jianfeng
关键词Protein-coding Regions Microbial Genomes Dna Sequences Diversity Obesity Flora
学科领域Physics
资助者National Natural Science Foundation of China [11175224, 11121403] ; National Natural Science Foundation of China [11175224, 11121403] ; National Natural Science Foundation of China [11175224, 11121403] ; National Natural Science Foundation of China [11175224, 11121403]
DOI10.1016/j.compbiolchem.2014.08.016
URL查看原文
收录类别SCI
语种英语
资助者National Natural Science Foundation of China [11175224, 11121403] ; National Natural Science Foundation of China [11175224, 11121403] ; National Natural Science Foundation of China [11175224, 11121403] ; National Natural Science Foundation of China [11175224, 11121403]
WOS记录号WOS:000347580400014
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文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/15553
专题理论物理所2014年知识产出
通讯作者Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China.
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Zhu, JF,Zheng, WM,Zheng, WM . Self-organizing approach for meta-genomes[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2014,53(Part A):118-124.
APA Zhu, JF,Zheng, WM,&Zheng, WM .(2014).Self-organizing approach for meta-genomes.COMPUTATIONAL BIOLOGY AND CHEMISTRY,53(Part A),118-124.
MLA Zhu, JF,et al."Self-organizing approach for meta-genomes".COMPUTATIONAL BIOLOGY AND CHEMISTRY 53.Part A(2014):118-124.
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