Prophage Hunter: an integrative hunting tool for active prophages.

Journal Article (Journal Article)

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

Full Text

Duke Authors

Cited Authors

  • Song, W; Sun, H-X; Zhang, C; Cheng, L; Peng, Y; Deng, Z; Wang, D; Wang, Y; Hu, M; Liu, W; Yang, H; Shen, Y; Li, J; You, L; Xiao, M

Published Date

  • July 2019

Published In

Volume / Issue

  • 47 / W1

Start / End Page

  • W74 - W80

PubMed ID

  • 31114893

Pubmed Central ID

  • PMC6602508

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

International Standard Serial Number (ISSN)

  • 0305-1048

Digital Object Identifier (DOI)

  • 10.1093/nar/gkz380


  • eng