title: Global comparison of multiple-segmented viruses in 12-dimensional genome space.
abstract: We have recently developed a computational approach in a vector space for genome-based virus classification. This approach, called the "Natural Vector (NV) representation", which is an alignment-free method, allows us to classify single-segmented viruses with high speed and accuracy. For multiple-segmented viruses, typically phylogenetic trees of each segment are reconstructed for discovering viral phylogeny. Consensus tree methods may be used to combine the phylogenetic trees based on different segments. However, consensus tree methods were not developed for instances where the viruses have different numbers of segments or where their segments do not match well. We propose a novel approach for comparing multiple-segmented viruses globally, even in cases where viruses contain different numbers of segments. Using our method, each virus is represented by a set of vectors in R(12). The Hausdorff distance is then used to compare different sets of vectors. Phylogenetic trees can be reconstructed based on this distance. The proposed method is used for predicting classification labels of viruses with n-segments (n ⩾ 1). The correctness rates of our predictions based on cross-validation are as high as 96.5%, 95.4%, 99.7%, and 95.6% for Baltimore class, family, subfamily, and genus, respectively, which are comparable to the rates for single-segmented viruses only. Our method is not affected by the number or order of segments. We also demonstrate that the natural graphical representation based on the Hausdorff distance is more reasonable than the consensus tree for a recent public health threat, the influenza A (H7N9) viruses.
authors.affiliation: Department of Statistics, University of Central Florida, Orlando, FL 32816, USA.
authors.forename: Hsin-Hsiung
authors.initials: HH
authors.lastname: Huang
authors.affiliation: Mind-Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, South Australia 5000, Australia.
authors.forename: Chenglong
authors.initials: C
authors.lastname: Yu
authors.affiliation: Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Civis Analytics, Chicago, IL, USA.
authors.forename: Troy
authors.initials: T
authors.lastname: Hernandez
authors.affiliation: Information Technology Services Center, Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong.
authors.forename: Shek-Chung
authors.initials: SC
authors.lastname: Yau
authors.affiliation: Department of Biological Sciences, Chicago State University, Chicago, IL 60628, USA.
authors.forename: Rong Lucy
authors.initials: RL
authors.lastname: He
authors.affiliation: Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Yang
authors.affiliation: Department of Mathematical Sciences, Tsinghua University, Beijing 100084, PR China. Electronic address: yau@uic.edu.
authors.forename: Stephen S-T
authors.initials: SS
authors.lastname: Yau
mesh_terms: D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D064766:Influenza A Virus, H7N9 Subtype / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D014780:Viruses / Q000145:classification / Q000235:genetics
keywords: Natural graphical representation; Natural vector; Nucleotide sequence; Phylogeny