Prophage Hunter: an integrative hunting tool for active prophages

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 b...

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Bibliographic Details
Published in:Nucleic acids research 2019-07, Vol.47 (W1), p.W74-W80
Main Authors: Song, Wenchen, Sun, Hai-Xi, Zhang, Carolyn, Cheng, Li, Peng, Ye, Deng, Ziqing, Wang, Dan, Wang, Yun, Hu, Ming, Liu, Wenen, Yang, Huanming, Shen, Yue, Li, Junhua, You, Lingchong, Xiao, Minfeng
Format: Article
Language:English
Subjects:
Bacteriophages - genetics
Genome, Bacterial - genetics
Internet
Phylogeny
Prophages - genetics
Software
Web Server Issue
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Summary: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/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkz380