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Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences

Journal of computational biology : a journal of computational molecular cell biology | 6 May 2019

D Lebatteux, AM Remita and AB Diallo
Abstract
The classification of pathogens in emerging and re-emerging viruses represents major interests in taxonomic studies, functional genomics, host-pathogen interplay, prevention, and disease treatments. It consists of assigning a given sequence to its related group of known sequences sharing similar characteristics and traits. The challenges to such classification could be associated with several virus properties including recombination, mutation rate, multiplicity of motifs, and diversity. In domains such as pathogen monitoring and surveillance, it is important to detect and quantify known and novel taxa without exploiting the full and accurate alignments or virus family profiles. In this study, we propose an alignment-free method, CASTOR-KRFE, to detect discriminating subsequences within known pathogen sequences to classify accurately unknown pathogen sequences. This method includes three major steps: (1) vectorization of known viral genomic sequences based on k-mers to constitute the potential features, (2) efficient way of pattern extraction and evaluation maximizing classification performance, and (3) prediction of the minimal set of features fitting a given criterion (threshold of performance metric and maximum number of features). We assessed this method through a jackknife data partitioning on a dozen of various virus data sets, covering the seven major virus groups and including influenza virus, Ebola virus, human immunodeficiency virus 1, hepatitis C virus, hepatitis B virus, and human papillomavirus. CASTOR-KRFE provides a weighted average F-measure >0.96 over a wide range of viruses. Our method also shows better performance on complex virus data sets than multiple subsequences extractor for classification (MISSEL), a subsequence extraction method, and the Discriminative mode of MEME patterns extraction tool.
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