ArticleNucleic acids research2021
Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 23 citations in OpenAlex.
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- V- and VNature communications · 2026Article
- Safety and probiotic characterization ofFrontiers in microbiology · 2026Article
- Systematic evaluation of phenotypic variations induced by prophages in a clinical isolate ofmSystems · 2025Article
- MRDadaptis: self-adaptive parameter configuration enhances minimal residual disease detection in heterogeneous ctDNA samples.Briefings in bioinformatics · 2025Article
- Highly accurate prophage island detection with PIDE.Genome biology · 2025Article
- A nuclease domain fused to the Snf2 helicase confers antiphage defence in coral-associated Halomonas meridiana.Microbial biotechnology · 2024Article
- VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes.NAR genomics and bioinformatics · 2024Article
- Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria.Applied and environmental microbiology · 2024Article
- Active prophages in coral-associated Halomonas capable of lateral transduction.The ISME journal · 2024Article
- Genomic characterization of SNW-1, a novel prophage of the deep-sea vent chemolithoautotroph Sulfurimonas indica NW79.Genetics and molecular biology · 2024Article
- Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria.The ISME journal · 2023Article
- VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes.bioRxiv : the preprint server for biology · 2023Article
- A systematic analysis of marine lysogens and proviruses.Nature communications · 2023Article
- A multidrug-resistantMicrobial genomics · 2023Article
- Comparative Genomic Analysis of Cold-Water Coral-DerivedMarine drugs · 2023Article
- The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction.Nature ecology & evolution · 2022Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The life cycle of temperate phages includes a lysogenic cycle stage when the phage integrates into the host genome and becomes a prophage. However, the identification of prophages that are highly divergent from known phages remains challenging. In this study, by taking advantage of the lysis-lysogeny switch of temperate phages, we designed Prophage Tracer, a tool for recognizing active prophages in prokaryotic genomes using short-read sequencing data, independent of phage gene similarity searching. Prophage Tracer uses the criterion of overlapping split-read alignment to recognize discriminative reads that contain bacterial (attB) and phage (attP) att sites representing prophage excision signals. Performance testing showed that Prophage Tracer could predict known prophages with precise boundaries, as well as novel prophages. Two novel prophages, dsDNA and ssDNA, encoding highly divergent major capsid proteins, were identified in coral-associated bacteria. Prophage Tracer is a reliable data mining tool for the identification of novel temperate phages and mobile genetic elements. The code for the Prophage Tracer is publicly available at https://github.com/WangLab-SCSIO/Prophage_Tracer.
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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.