MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool
文献类型：期刊论文
| 作者 | Zou, Bin1; Li, JieFu1; Zhou, Quan1; Quan, Zhe-Xue1; Li, JieFu2; , |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2017 |
| 卷号 | 12期号:3页码:e0174609 |
| 关键词 | Esophageal adenocarcinama (EAC) Prognosis Biomarker CRNKL1 |
| ISSN号 | 1932-6203 |
| DOI | 10.1371/journal.pone.0174609 |
| 文献子类 | Article |
| 英文摘要 | An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers. However, the use of short reads obtained through next-generation sequencing for primer evaluation has not been well resolved. The software MIPE (MIcrobiota metagenome Primer Explorer) was developed to adapt numerous short reads from metagenomes and metatranscriptomes. Using metagenomic or metatranscriptomic datasets as input, MIPE extracts and aligns rRNA to reveal detailed information on microbial composition and evaluate SSU rRNA primers. A mock dataset, a real Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) test dataset, two PrimerProspector test datasets and a real metatranscriptomic dataset were used to validate MIPE. The software calls Mothur (v1.33.3) and the SILVA database (v119) for the alignment and classification of rRNA genes from a metagenome or metatranscriptome. MIPE can effectively extract shotgun rRNA reads from a metagenome or metatranscriptome and is capable of classifying these sequences and exhibiting sensitivity to different SSU rRNA PCR primers. Therefore, MIPE can be used to guide primer design for specific environmental samples. |
| 学科主题 | Science & Technology - Other Topics |
| WOS关键词 | RIBOSOMAL-RNA GENE ; SEQUENCING DATA ; DIVERSITY ; PCR ; RESOURCE ; DATABASE ; MISMATCH ; GENOMES ; DESIGN ; SAMPLE |
| 语种 | 英语 |
| WOS记录号 | WOS:000399174400065 |
| 出版者 | PUBLIC LIBRARY SCIENCE |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1231]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Fudan Univ, Sch Life Sci, Dept Microbiol & Microbial Engn, Shanghai, Peoples R China; 2.Chinese Acad Sci, CAS MPG Partner Inst Computat Biol PICB, Shanghai Inst Biol Sci, Shanghai, Peoples R China, |
| 推荐引用方式 GB/T 7714 | Zou, Bin,Li, JieFu,Zhou, Quan,et al. MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool[J]. PLOS ONE,2017,12(3):e0174609. |
| APA | Zou, Bin,Li, JieFu,Zhou, Quan,Quan, Zhe-Xue,Li, JieFu,&,.(2017).MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool.PLOS ONE,12(3),e0174609. |
| MLA | Zou, Bin,et al."MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool".PLOS ONE 12.3(2017):e0174609. |
入库方式： OAI收割
来源：上海营养与健康研究所
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