identification and typing of human enterovirus a genomic barcode approach识别和人类肠道病毒基因组条形码方法的输入.pdfVIP

Identification and Typing of Human Enterovirus: A Genomic Barcode Approach 1. 1. 3 1 4 2,3 1 Chengguo Wei , Guoqing Wang , Xin Chen , Honglan Huang , Bin Liu , Ying Xu *, Fan Li * 1 Department of Pathogeny Biology, Norman Bethune Medical College of Jilin University, Changchun, Jilin, China, 2 Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America, 3 College of Computer Science and Technology, Jilin University, Changchun, Jilin, China, 4 The First Bethune Hospital of Jilin University, Changchun, Jilin, China Abstract Identification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HEV or other human viruses, for a fixed k, 1,k,7, where a genome barcode is defined in terms of the k- mer frequency distribution across the whole genome for all combinations of k-mers. A phylogenetic tree is constructed using a barcode-based distance and a neighbor-joining method among a set of 443 representative non-HEV human viruses and 395 HEV sequences. The tree shows a clear separation of the HEV viruses from all the non-HEV viruses with 100% accuracy and a separation