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题名: Self-organizing approach for meta-genomes
作者: Zhu, JF ;  Zheng, WM
刊名: COMPUTATIONAL BIOLOGY AND CHEMISTRY
出版日期: 2014
卷号: 53, 期号:Part A, 页码:118-124
关键词: PROTEIN-CODING REGIONS ;  MICROBIAL GENOMES ;  DNA ;  SEQUENCES ;  DIVERSITY ;  OBESITY ;  FLORA
学科分类: Physics
DOI: 10.1016/j.compbiolchem.2014.08.016
通讯作者: Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China.
部门归属: [Zhu, Jianfeng
英文摘要: 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.
资助者: National Natural Science Foundation of China [11175224, 11121403]
收录类别: SCI
原文出处: 查看原文
语种: 英语
WOS记录号: WOS:000347580400014
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/15553
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Recommended Citation:
Zhu, JF,Zheng, WM. Self-organizing approach for meta-genomes[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2014,53(Part A):118-124.
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