HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes.

Abstract

We present HoPhage (Host of Phage) to identify the host of a given phage fragment from metavirome data at the genus level. HoPhage integrates two modules using a deep learning algorithm and a Markov chain model, respectively. HoPhage achieves 47.90% and 82.47% mean accuracy at the genus and phylum levels for ∼1-kb long artificial phage fragments when predicting host among 50 genera, representing 7.54-20.22% and 13.55-24.31% improvement, respectively. By testing on three real virome samples, HoPhage yields 81.11% mean accuracy at the genus level within a much broader candidate host range. HoPhage is available at http://cqb.pku.edu.cn/ZhuLab/HoPhage/data/. Supplementary data are available at Bioinformatics online.