Prophage Hunter: an integrative hunting tool for active prophages

Wenchen Song; Hai-Xi Sun; Carolyn Zhang; Li Cheng; Ye Peng; Ziqing Deng; Dan Wang; Yun Wang; Ming Hu; Wenen Liu; Huanming Yang; Yue Shen; Junhua Li; Lingchong You; Minfeng Xiao

doi:10.1093/nar/gkz380

Prophage Hunter: an integrative hunting tool for active prophages

Nucleic Acids Res. 2019 Jul 2;47(W1):W74-W80. doi: 10.1093/nar/gkz380.

Authors

Wenchen Song^{1

2

3}, Hai-Xi Sun^{1

2}, Carolyn Zhang⁴, Li Cheng^{1

2

5}, Ye Peng^{1

2

5}, Ziqing Deng^{1

2}, Dan Wang^{1

2}, Yun Wang^{1

2}, Ming Hu³, Wenen Liu⁶, Huanming Yang^{1

2}, Yue Shen^{1

2}, Junhua Li^{1

2

5}, Lingchong You^{4

7

8}, Minfeng Xiao^{1

2}

Affiliations

¹ BGI-Shenzhen, Shenzhen 518083, China.
² China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.
³ Department of Basic Medical Sciences, Qingdao University, Qingdao 266071, China.
⁴ Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
⁵ South China University of Technology, Guangzhou, Guangdong 510640, China.
⁶ Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China.
⁷ Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.
⁸ Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.

Abstract

Identifying active prophages is critical for studying coevolution of phage and bacteria, investigating phage physiology and biochemistry, and engineering designer phages for diverse applications. We present Prophage Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria. Combining sequence similarity-based matching and genetic features-based machine learning classification, we developed a novel scoring system that exhibits higher accuracy than current tools in predicting active prophages on the validation datasets. The option of skipping similarity matching is also available so that there's higher chance for novel phages to be discovered. Prophage Hunter provides a one-stop web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and annotate the function of phage proteins. Prophage Hunter is freely available at https://pro-hunter.bgi.com/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages / genetics*
Genome, Bacterial / genetics*
Internet
Phylogeny
Prophages / genetics*
Software*