ArticleNucleic acids research2021
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types.
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 156 papers.
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156 citing papers in PubMed.
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- Structural insights into type-I and type-II Lamassu antiphage systems.Nature chemical biology · 2026Article
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.PLoS computational biology · 2026Article
- A syntenic pangenome of Gardnerella reveals novel plasmids and phage, taxonomic boundaries, and species-level stratification of metabolic and virulence potential.Nature communications · 2026Article
- Eco-evolutionary feedbacks drive the co-occurrence of restriction-modification systems and antimicrobial resistance genes in bacteria.PLoS biology · 2026Article
- Antiphage defence systems Druantia III and Zorya II synergise via shared DNA intermediates in a phage-specific manner.bioRxiv : the preprint server for biology · 2026Article
- Isolation and characterization of broad-rangeMicrobiology (Reading, England) · 2026Article
- Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.Environmental microbiome · 2026Article
- DefensePredictor: A machine learning model to discover prokaryotic immune systems.Science (New York, N.Y.) · 2026Article
- Engineered phages evade the complete defense repertoire of highly phage-resistant MRSA clinical isolates.bioRxiv : the preprint server for biology · 2026Article
- Tmn blocks phage spread via plasmolysis and triggers synergistic defence responses.bioRxiv : the preprint server for biology · 2026Article
96 more citing papers are in PubMed but not listed here.
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).
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