Self-organizing approach for meta-genomes
文献类型：期刊论文
| 作者 | 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 |
| 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 |
| 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. |
入库方式： OAI收割
来源：理论物理研究所
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