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Zhu, JF; Zheng, WM; Zheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China.
Self-organizing approach for meta-genomes
Source PublicationCOMPUTATIONAL BIOLOGY AND CHEMISTRY
Language英语
KeywordProtein-coding Regions Microbial Genomes Dna Sequences Diversity Obesity Flora
AbstractWe 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.
2014
ISSN1476-9271
Volume53Issue:Part APages:118-124
Subject AreaPhysics
DOI10.1016/j.compbiolchem.2014.08.016
Indexed BySCI
Funding OrganizationNational 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]
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Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/15553
Collection理论物理所科研产出_SCI论文
Corresponding AuthorZheng, WM (reprint author), Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China.
Recommended Citation
GB/T 7714
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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