The defense system prediction tool has been updated to DefenseFinder 2.0.0 on the MicroScope platform. In this context, the results of AntiDefenseFinder have been integrated.
DefenseFinder is a bioinformatic tool for the systematic detection of anti-phage defense systems in prokaryotic genomes. It employs MacSyFinder and curated HMM profiles to identify known bacterial immunity mechanisms. The tool analyzes protein or nucleic sequences to find clusters of genes that constitute functional defense units. The decision rules are typically defined by a list of mandatory, accessory, or forbidden proteins necessary for the detection of a each system.
- a broad range of anti-phage systems from the models DefenseFinder 2.0.2 : Avs, Azaca, BREX, DdmDE, Dodola, DRT, RADAR, RM, RosmerTA, SanaTA, Viperin, …
- CRISPR-Cas systems based on models CasFinder 3.1.0 containing 535 HMM proteins profiles. It allows the detection 6 different types and 37 different subtypes of CRISPR-Cas systems.
- antidefense systems corresponding to known inhibitors of prokaryotic defense systems.
These prediction results can be seen in the Prophages & Defense Systems page from the Comparative Genomics section. They can also be queried in the Search by keyword functionality. Finally, the are integrated in the results of pangenomes on the Pangenomes RGPs page. You may also refer to the DefenseFinder section of the MicroScope User documentation for further information.
References
- “Systematic and quantitative view of the antiviral arsenal of prokaryotes” Nature Communication, 2022, Tesson F., Hervé A. , Mordret E., Touchon M., d’Humières C., Cury J., Bernheim A.
- “MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes.” Peer Community Journal, Volume 3 (2023), article no. e28. Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S.
- “CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.” Nucleic Acids Research 2018 Couvin D. et al.
- “Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements” Nucleic Acids Research, Volume 53, Issue 1, 13 January 2025, Florian Tesson, Erin Huiting, Linlin Wei, Jie Ren, Matthew Johnson, Rémi Planel, Jean Cury, Yue Feng, Joseph Bondy-Denomy, Aude Bernheim.
Please report us any bugs you may meet.