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

Abstract:

: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.

journal_name

J Virol Methods

authors

Kolekar P,Hake N,Kale M,Kulkarni-Kale U

doi

10.1016/j.jviromet.2013.12.012

subject

Has Abstract

pub_date

2014-03-01 00:00:00

pages

41-55

eissn

0166-0934

issn

1879-0984

pii

S0166-0934(13)00514-4

journal_volume

198

pub_type

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