HoPhage: anab initiotool for identifying hosts of phage fragments from metaviromes

• DOI: 10.1093/bioinformatics/btab585
• Publication Date: 2021-08-10T19:12:02Z
• Authors: Jie Tan; Zhencheng Fang; Shufang Wu; Qian Guo; Xiaoqing Jiang; Huaiqiu Zhu
• Keywords: 0303 health sciences; 03 medical and health sciences; Bacteriophages; Applications Notes; Algorithms; Markov Chains; Software

AbstractSummaryWe 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.Availability and implementationHoPhage is available at http://cqb.pku.edu.cn/ZhuLab/HoPhage/data/Supplementary informationSupplementary data are available at Bioinformatics online.