WNV Typer: A server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution

• Published in: Journal of virological methods 2014-03, Vol.198, p.41-55
• Main Authors: Kolekar, Pandurang, Hake, Nilesh, Kale, Mohan, Kulkarni-Kale, Urmila
• Format: Article
• Language: English
• Subjects: Alignment-free; Bioinformatics; Genome, Viral - genetics; Genotype; Genotyping; Phylogeny; Return time distribution; Sequence Analysis - methods; West Nile Fever - virology; West Nile virus; West Nile virus - genetics
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2013.12.012

•Web server is developed for genotyping of West Nile viruses using genomic sequences.•The server uses alignment-free method for genotyping of West Nile viruses.•The method is based on return time distribution and is developed in-house.•The method has 100% sensitivity and specificity for the genotyping.•Web server is expected to assist epidemiological surveillance of West Nile viruses. West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity.