Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
Yang, Bo1; Wang, Yong2; Qian, Pei-Yuan1
2016-03-18
Source PublicationBMC BIOINFORMATICS
Volume17
AbstractBackground: 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.
SubtypeArticle
Keyword16s Rrna 16s Rrna Gene Variable Regions Phylogenetic Geodesic Distance Primer
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
DOI10.1186/s12859-016-0992-y
Indexed BySCI
Language英语
WOS KeywordGRADIENT GEL-ELECTROPHORESIS ; CONSERVED 690 HAIRPIN ; COMPUTING GEODESIC DISTANCES ; ESCHERICHIA-COLI ; MICROBIAL COMMUNITIES ; ANGSTROM RESOLUTION ; PCR PRIMERS ; TREE SPACE ; NUCLEOTIDES ; CYANOBACTERIA
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS IDWOS:000372487500001
Citation statistics
Cited Times:75[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.idsse.ac.cn/handle/183446/1531
Collection深海科学研究部_深海生物学研究室_海洋微生物宏基因组与分子进化研究组
Affiliation1.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
Recommended Citation
GB/T 7714
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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