title: Clustering DNA sequences using the out-of-place measure with reduced n-grams.
abstract: The alignment-free n-gram based method with the out-of-place measures as the distance has been successfully applied to automatic text or natural languages categorization in real time. However, it is not clear about its performance and the selection of n for comparing genome sequences. Here we propose a symmetric version of the out-of-place measure and a new approach for finding the optimal range of n to construct a phylogenetic tree with the symmetric out-of-place measures. Our method is then applied to real genome sequence datasets. The resulting phylogenetic trees are matching with the standard biological classification. It shows that our proposed method is a very powerful tool for phylogenetic analysis in terms of both classification accuracy and computation efficiency.
authors.affiliation: Department of Statistics, University of Central Florida, Orlando, FL 32816, USA. Electronic address: hsin.huang@ucf.edu.
authors.forename: Hsin-Hsiung
authors.initials: HH
authors.lastname: Huang
authors.affiliation: Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Flinders University, Adelaide, SA 5001, Australia.
authors.forename: Chenglong
authors.initials: C
authors.lastname: Yu
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D010802:Phylogeny; D011323:Primates / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D014714:Vertebrates / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D012336:RNA, Ribosomal, 16S
keywords: Alignment-free method; Out-of-place measure; Phylogenetic analysis; Reduced n-gram