Prophage Hunter: an integrative hunting tool for active prophages

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Active prophages are crucial for understanding phage-bacteria coevolution, phage biology, and developing engineered phages.
• Accurate identification of active prophages from bacterial genomes is essential for these research areas.

Purpose of the Study:

• To develop a novel computational tool, Prophage Hunter, for identifying active prophages within bacterial genomes.
• To improve the accuracy of active prophage prediction compared to existing methods.
• To provide a comprehensive web service for prophage analysis, including extraction, activity evaluation, and functional annotation.

Main Methods:

• Prophage Hunter combines sequence similarity matching with machine learning classification based on genetic features.
• A novel scoring system was developed to enhance prediction accuracy.
• An option to bypass similarity matching was included to facilitate the discovery of novel phages.

Main Results:

• The developed scoring system demonstrated higher accuracy in predicting active prophages on validation datasets compared to current tools.
• Prophage Hunter successfully extracts prophage genomes, evaluates their activity, identifies related phages, and annotates phage proteins.
• The tool offers a user-friendly web service for comprehensive prophage analysis.

Conclusions:

• Prophage Hunter is an accurate and versatile tool for identifying active prophages in bacterial genomes.
• The tool facilitates research in phage biology, phage-bacteria interactions, and phage engineering.
• Prophage Hunter is freely accessible, promoting wider adoption and advancing the field.