A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

作者: Nam-Phuong Nguyen , Tandy Warnow , Mihai Pop , Bryan White

DOI: 10.1038/NPJBIOFILMS.2016.4

关键词:

摘要: … Sequences are clustered into bins called ‘Operational Taxonomic Units’ (OTUs) based upon similarity. Typically, the similarity between a pair of sequences is computed as the …

参考文章(35)
S. Tavare, Some probabilistic and statistical problems in the analysis of DNA sequences Some mathematical questions in biology / DNA sequence analysis edited by Robert M. Miura. ,(1986)
Nam-phuong D. Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy Warnow, Ultra-large alignments using phylogeny-aware profiles Genome Biology. ,vol. 16, pp. 124- 124 ,(2015) , 10.1186/S13059-015-0688-Z
Michael D Harwich, Myrna G Serrano, Jennifer M Fettweis, Jao M Alves, Mark A Reimers, Vaginal Microbiome Consortium (additional members), Gregory A Buck, Jefferson Kimberly K, None, Genomic sequence analysis and characterization of Sneathia amnii sp. nov BMC Genomics. ,vol. 13, pp. 1- 15 ,(2012) , 10.1186/1471-2164-13-S8-S4
Sarah P. Preheim, Allison R. Perrotta, Antonio M. Martin-Platero, Anika Gupta, Eric J. Alm, Distribution-based clustering: using ecology to refine the operational taxonomic unit. Applied and Environmental Microbiology. ,vol. 79, pp. 6593- 6603 ,(2013) , 10.1128/AEM.00342-13
Nikhil Chaudhary, Ashok K Sharma, Piyush Agarwal, Ankit Gupta, Vineet K Sharma, None, 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets. PLOS ONE. ,vol. 10, ,(2015) , 10.1371/JOURNAL.PONE.0116106
Susan M. Huse, Les Dethlefsen, Julie A. Huber, David Mark Welch, David A. Relman, Mitchell L. Sogin, Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing PLoS Genetics. ,vol. 4, pp. e1000255- ,(2008) , 10.1371/JOURNAL.PGEN.1000255
Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin, FastTree 2--approximately maximum-likelihood trees for large alignments. PLOS ONE. ,vol. 5, ,(2010) , 10.1371/JOURNAL.PONE.0009490
S. MIRARAB, N. NGUYEN, T. WARNOW, SEPP: SATé-enabled phylogenetic placement. pacific symposium on biocomputing. pp. 247- 258 ,(2011) , 10.1142/9789814366496_0024
Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy Warnow, PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences Journal of Computational Biology. ,vol. 22, pp. 377- 386 ,(2015) , 10.1089/CMB.2014.0156