title: Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.
abstract: The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.
authors.affiliation: UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.|Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA.|Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
authors.forename: Se-Ran
authors.initials: SR
authors.lastname: Jun
authors.affiliation: Joint Institute for Computational Sciences, University of Tennessee, Knoxville, TN 37831, USA.|Computational Biomolecular Modeling and Bioinformatics Group, Computer Science and Mathematics Division, Oak Ridge National Laboratories, Oak Ridge, TN 37831, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Leuze
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA.|Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
authors.forename: David
authors.initials: D
authors.lastname: Ussery
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA.|Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
authors.forename: Intawat
authors.initials: I
authors.lastname: Nookaew
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D059646:Genome Size; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D014780:Viruses / Q000145:classification* / Q000235:genetics*; D000073336:Whole Genome Sequencing