Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
Yang, Bo1; Wang, Yong2; Qian, Pei-Yuan1
2016-03-18
发表期刊BMC BIOINFORMATICS
卷号17
摘要Background: Prokaryotic 16S ribosomal RNA (rRNA) sequences are widely used in environmental microbiology and molecular evolution as reliable markers for the taxonomic classification and phylogenetic analysis of microbes. Restricted by current sequencing techniques, the massive sequencing of 16S rRNA gene amplicons encompassing the full length of genes is not yet feasible. Thus, the selection of the most efficient hypervariable regions for phylogenetic analysis and taxonomic classification is still debated. In the present study, several bioinformatics tools were integrated to build an in silico pipeline to evaluate the phylogenetic sensitivity of the hypervariable regions compared with the corresponding full-length sequences.
文章类型Article
关键词16s Rrna 16s Rrna Gene Variable Regions Phylogenetic Geodesic Distance Primer
WOS标题词Science & Technology ; Life Sciences & Biomedicine
DOI10.1186/s12859-016-0992-y
收录类别SCI
语种英语
关键词[WOS]GRADIENT GEL-ELECTROPHORESIS ; CONSERVED 690 HAIRPIN ; COMPUTING GEODESIC DISTANCES ; ESCHERICHIA-COLI ; MICROBIAL COMMUNITIES ; ANGSTROM RESOLUTION ; PCR PRIMERS ; TREE SPACE ; NUCLEOTIDES ; CYANOBACTERIA
WOS类目Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号WOS:000372487500001
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被引频次:56[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.idsse.ac.cn/handle/183446/1531
专题深海科学研究部_深海生物学研究室_海洋微生物宏基因与分子进化研究组
作者单位1.Hong Kong Univ Sci & Technol, Div Life Sci, Hong Kong, Hong Kong, Peoples R China
2.Chinese Acad Sci, Sanya Inst Deep Sea Sci & Engn, San Ya, Hai Nan, Peoples R China
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Yang, Bo,Wang, Yong,Qian, Pei-Yuan. Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis[J]. BMC BIOINFORMATICS,2016,17.
APA Yang, Bo,Wang, Yong,&Qian, Pei-Yuan.(2016).Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis.BMC BIOINFORMATICS,17.
MLA Yang, Bo,et al."Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis".BMC BIOINFORMATICS 17(2016).
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