ArticleNucleic acids research2022
DEPhT: a novel approach for efficient prophage discovery and precise extraction.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- Article
- A novel phage satellite class induces prophage excision in Mycolicibacterium aichiense.Virology · 2026Article
- V- and VNature communications · 2026Article
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.bioRxiv : the preprint server for biology · 2026Article
- A novel phage satellite class induces prophage excision inbioRxiv : the preprint server for biology · 2025Article
- Effects of bacteriophages on gut microbiome functionality.Gut microbes · 2025Review
- Genome synthesis, assembly, and rebooting of therapeutically useful high G+C% mycobacteriophages.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- All the world's a phage.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Engineering Phages to Fight Multidrug-Resistant Bacteria.Chemical reviews · 2025Review
- Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.Environmental microbiome · 2025Article
- Use of epigenetically modified bacteriophage and dual beta-lactams to treat a Mycobacterium abscessus sternal wound infection.Nature communications · 2024Article
- Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments.Nature communications · 2024Article
- A Bioinformatic Ecosystem for Bacteriophage Genomics: PhaMMSeqs, Phamerator, pdm_utils, PhagesDB, DEPhT, and PhamClust.Viruses · 2024Review
- Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages.bioRxiv : the preprint server for biology · 2024Article
- Article
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6 authors.
Funding
Abstract
Advances in genome sequencing have produced hundreds of thousands of bacterial genome sequences, many of which have integrated prophages derived from temperate bacteriophages. These prophages play key roles by influencing bacterial metabolism, pathogenicity, antibiotic resistance, and defense against viral attack. However, they vary considerably even among related bacterial strains, and they are challenging to identify computationally and to extract precisely for comparative genomic analyses. Here, we describe DEPhT, a multimodal tool for prophage discovery and extraction. It has three run modes that facilitate rapid screening of large numbers of bacterial genomes, precise extraction of prophage sequences, and prophage annotation. DEPhT uses genomic architectural features that discriminate between phage and bacterial sequences for efficient prophage discovery, and targeted homology searches for precise prophage extraction. DEPhT is designed for prophage discovery in Mycobacterium genomes but can be adapted broadly to other bacteria. We deploy DEPhT to demonstrate that prophages are prevalent in Mycobacterium strains but are absent not only from the few well-characterized Mycobacterium tuberculosis strains, but also are absent from all ∼30 000 sequenced M. tuberculosis strains.
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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.