ArticleScientific reports2017
PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 510 papers.
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510 citing papers in PubMed.
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- Isolation and characterization of a novel Schitoviridae phage VipHU7 that infects Vibrio parahaemolyticus.Archives of virology · 2026Article
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- Isolation, characterization, and genomic analysis of a novel lytic bacteriophage with potent antibiofilm activity against multidrug-resistant Acinetobacter baumannii.BMC microbiology · 2026Article
- Dose-and regimen-dependent therapeutic efficacy of the lytic Klebsiella phage TRK61 in a Galleria mellonella infection model.Archives of virology · 2026Article
- Genome sequence of theMicrobiology resource announcements · 2026Article
- Genomic and Biological Characterization of a Broad-Host-Range KVP40-Like Bacteriophage vB_VpM-pA3B5 for Control of AHPND-CausingJournal of microbiology and biotechnology · 2026Article
- Genomic characterization of three novel Shiga toxin-producing Escherichia coli lytic phages.Archives of virology · 2026Article
- Molecular and biological characterization of a newly discovered Kayfunavirus bacteriophage targeting multidrug-resistant Escherichia coli from swine feces.Scientific reports · 2026Article
- Genome sequences of 19Microbiology resource announcements · 2026Article
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450 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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Abstract
The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data. Our method relies on the detection of biases in the number of reads, which are observable at natural DNA termini compared with the rest of the phage genome. We implemented our method with the creation of the software PhageTerm and validated it using a set of phages with well-established packaging mechanisms representative of the termini diversity, i.e. 5'cos (Lambda), 3'cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of nine Clostridium difficile phages and six phages whose sequences were retrieved from the Sequence Read Archive. PhageTerm is freely available (https://sourceforge.net/projects/phageterm), as a Galaxy ToolShed and on a Galaxy-based server (https://galaxy.pasteur.fr).
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