Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus

Scientific Reports
Wojciech GałanMałgorzata Jakubowska

Abstract

Recent advances in metagenomics provided a valuable alternative to culture-based approaches for better sampling viral diversity. However, some of newly identified viruses lack sequence similarity to any of previously sequenced ones, and cannot be easily assigned to their hosts. Here we present a bioinformatic approach to this problem. We developed classifiers capable of distinguishing eukaryotic viruses from the phages achieving almost 95% prediction accuracy. The classifiers are wrapped in Host Taxon Predictor (HTP) software written in Python which is freely available at https://github.com/wojciech-galan/viruses_classifier . HTP's performance was later demonstrated on a collection of newly identified viral genomes and genome fragments. In summary, HTP is a culture- and alignment-free approach for distinction between phages and eukaryotic viruses. We have also shown that it is possible to further extend our method to go up the evolutionary tree and predict whether a virus can infect narrower taxa.

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Citations

May 27, 2020·PLoS Computational Biology·Francesca YoungDavid L Robertson
Jul 17, 2020·Computational and Structural Biotechnology Journal·Varada KhotAlyse K Hawley
Jul 6, 2020·Trends in Microbiology·Mohammadali Khan MirzaeiLi Deng
Feb 9, 2021·NAR Genomics and Bioinformatics·Jakub M BartoszewiczBernhard Y Renard

Methods Mentioned

BETA
feature extraction

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