| name | padloc |
| description | PADLOC (Prokaryotic Antiviral Defence LOCator) — HMM + synteny detection of antiviral defence systems (CRISPR-Cas and many other systems) in prokaryotic genomes. Use as a complement or alternative to DefenseFinder for defenseome surveys. Upstream: https://github.com/padlocbio/padloc. DB: https://github.com/padlocbio/padloc-db. Web: https://padloc.otago.ac.nz. Route via microbial-mining; pair with genomad/virsorter2 for MGE context.
|
| license | MIT |
| category | analysis-tools |
| tags | ["PADLOC","defense","defenseome","CRISPR","antiviral","genome-mining"] |
| upstream | https://github.com/padlocbio/padloc |
| stage | mining |
PADLOC
Upstream: padlocbio/padloc ·
DB: padloc-db ·
Web: https://padloc.otago.ac.nz/padloc/
Citation
Payne, L. J. et al. Identification and classification of antiviral defence
systems in bacteria and archaea with PADLOC reveals new system types.
Nucleic Acids Res. 49, 10868–10878 (2021).
https://doi.org/10.1093/nar/gkab883
Web server: Payne, L. J. et al. PADLOC: a web server for the identification
of antiviral defence systems in microbial genomes. Nucleic Acids Res. 50,
W541–W550 (2022). https://doi.org/10.1093/nar/gkac400
See also docs/references.md.
Analytical thinking
PADLOC finds defence systems via HMM homology + system architecture/synteny.
Complements defensefinder (different model sets / system coverage). For dark
neighborhood discovery without known system models use spacedust.
| vs | Prefer PADLOC when |
|---|
defensefinder | PADLOC-DB models / web precomputes; cross-check both for surveys |
spacedust | Known antiviral system types vs de novo clusters |
genomad | Host defenseome vs MGE/virus contigs |
Annotate proteins first (bakta / prokka). Pin padloc-db version.
How to run
padloc --fna genome.fna --outdir padloc_out
Decision tree
Defenseome / antiviral systems?
├─ PADLOC models → padloc
├─ DefenseFinder models → defensefinder
├─ Prefer both for Methods robustness → padloc + defensefinder
├─ Dark conserved neighborhoods → spacedust
└─ Virus/plasmid contigs → genomad → checkv
Related skills
defensefinder · spacedust · genomad · virsorter2 · bakta ·
microbial-mining · tool-selection
