%0 Journal Article
%T Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping
%A Guohui Lin
%A Zhipeng Cai
%A Junfeng Wu
%A Xiu-Feng Wan
%A Lizhe Xu
%A Randy Goebel
%J BMC Bioinformatics
%D 2008
%I BioMed Central
%R 10.1186/1471-2105-9-279
%X We used 129 FMDV strains with known serotype as training strains to select as many as 140 most serotype-specific nucleotide strings. We then constructed a linear-kernel Support Vector Machine classifier using these 140 strings. Under the leave-one-out cross validation scheme, this classifier was able to assign correct serotype to 127 of these 129 strains, achieving 98.45% accuracy. It also assigned serotype correctly to an independent test set of 83 other FMDV strains downloaded separately from NCBI GenBank.Computational genotyping is much faster and much cheaper than the wet-lab based biological experiments, upon the availability of the detailed molecular sequences. The high accuracy of our proposed method suggests the potential of utilizing a few signature nucleotide strings instead of whole genomes to determine the serotypes of novel FMDV strains.Foot-and-mouth disease (FMD) is one of the most contagious animal diseases, with a large economic impact. Frequent sporadic outbreaks have been reported in many countries. The most recent outbreak in the United Kingdom costs tens of billions of dollars [1]. This disease causes extensive epidemics in domestic and wild cloven-hooved animals, such as cattle, sheep, goats, and pigs. In addition, it can result in persistent infections in ruminants, and so the disease is in the importation banning and detection list of most countries. Furthermore, this disease can cause mild infection in human through skin wounds or the oral mucosa. Therefore, once this disease is identified, the infected animals are always required to be destroyed. The vaccination is the most efficient method to prevent this disease, so preparation and selection of an efficient vaccine will be the most important for FMD prevention and control.FMD is caused by a single strand RNA virus, so-called FMD virus [2], which is a member of the family Picornaviridae, genus Aphthovirus. The genome of FMDV is about 8.4 kbp in size (including highly structured 5' and 3' u
%U http://www.biomedcentral.com/1471-2105/9/279