Self-organizing approach for meta-genomes

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	Self-organizing approach for meta-genomes
	Zheng, WM
刊名	COMPUTATIONAL BIOLOGY AND CHEMISTRY
	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
ISSN号	1476-9271
通讯作者	Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China.
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.
学科主题	Physics
收录类别	SCI
资助信息	National Natural Science Foundation of China [11175224, 11121403]
原文出处	http://dx.doi.org/10.1016/j.compbiolchem.2014.08.016
语种	英语
WOS记录号	WOS:000347580400014
公开日期	2015-06-03
内容类型	期刊论文
源URL	[http://ir.itp.ac.cn/handle/311006/15553]
专题	理论物理研究所_理论物理所1978-2010年知识产出
推荐引用方式 GB/T 7714	Zheng, WM. Self-organizing approach for meta-genomes[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2014,53(Part A):118-124.
APA	Zheng, WM.(2014).Self-organizing approach for meta-genomes.COMPUTATIONAL BIOLOGY AND CHEMISTRY,53(Part A),118-124.
MLA	Zheng, WM."Self-organizing approach for meta-genomes".COMPUTATIONAL BIOLOGY AND CHEMISTRY 53.Part A(2014):118-124.