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J Virol Methods. 2014 Mar;198:41-55. doi: 10.1016/j.jviromet.2013.12.012. Epub 2013 Dec 31.

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

Author information

1
Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: pandurang@bioinfo.net.in.
2
Bioinformatics Centre, University of Pune, Pune 411007, India.
3
Department of Statistics, University of Pune, Pune 411007, India. Electronic address: mmkale@stats.unipune.ac.in.
4
Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: urmila@bioinfo.net.in.

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.

KEYWORDS:

Alignment-free; Bioinformatics; Genotyping; Phylogeny; Return time distribution; West Nile virus

PMID:
24388930
DOI:
10.1016/j.jviromet.2013.12.012
[Indexed for MEDLINE]
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