ArticlePloS one2019
ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 57 citations in OpenAlex.
- V- and VNature communications · 2026Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Highly accurate prophage island detection with PIDE.Genome biology · 2025Article
- Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages.BMC microbiology · 2025Article
- Global diversity of enterococci and description of 18 previously unknown species.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tools and methodology toFrontiers in microbiology · 2024Review
- An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.Microbial ecology · 2023Article
- Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers.BMC genomics · 2023Article
- The Gonococcal Genetic Island defines distinct sub-populations ofMicrobial genomics · 2023Article
- The gut virome and the relevance of temperate phages in human health.Frontiers in cellular and infection microbiology · 2023Review
- Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo.Antibiotics (Basel, Switzerland) · 2022Article
- DEPhT: a novel approach for efficient prophage discovery and precise extraction.Nucleic acids research · 2022Article
- Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance.mSystems · 2022Article
- Computational Tools for the Analysis of Uncultivated Phage Genomes.Microbiology and molecular biology reviews : MMBR · 2022Review
- Metagenomic analysis of wastewater phageome from a University Hospital in Turkey.Archives of microbiology · 2022Article
- Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.Genome medicine · 2022Article
- Prophage-mediated genome differentiation of theMicrobial genomics · 2022Article
- Diversity of Pseudomonas aeruginosa Temperate Phages.mSphere · 2022Article
- YdfD, a Lysis Protein of the Qin Prophage, Is a Specific Inhibitor of the IspG-Catalyzed Step in the MEP Pathway ofInternational journal of molecular sciences · 2022Article
- In Silico Characterisation of Putative Prophages inMicroorganisms · 2022Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundProphages play a significant role in prokaryotic evolution, often altering the function of the cell that they infect via transfer of new genes e.g., virulence or antibiotic resistance factors, inactivation of existing genes or by modifying gene expression. Recently, phage therapy has gathered renewed interest as a promising alternative to control bacterial infections. Cataloging the repertoire of prophages in large collections of species' genomes is an important initial step in understanding their evolution and potential therapeutic utility. However, current widely-used tools for identifying prophages within bacterial genome sequences are mainly web-based, can have long response times, and do not scale to keep pace with the many thousands of genomes currently being sequenced routinely. METHODOLOGY: In this work, we present ProphET, an easy to install prophage predictor to be used in Linux operation system, without the constraints associated with a web-based tool. ProphET predictions rely on similarity searches against a database of prophage genes, taking as input a bacterial genome sequence in FASTA format and its corresponding gene annotation in GFF. ProphET identifies prophages in three steps: similarity search, calculation of the density of prophage genes, and edge refinement. ProphET performance was evaluated and compared with other phage predictors based on a set of 54 bacterial genomes containing 267 manually annotated prophages. FINDINGS AND
conclusionsProphET identifies prophages in bacterial genomes with high precision and offers a fast, highly scalable alternative to widely-used web-based applications for prophage detection.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.