A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
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Abstract
In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To facilitate the exploration of mechanistic, ecological, and evolutionary aspects related to antiphage defense systems, we released DefenseFinder in 2021 (Tesson et al., 2022). DefenseFinder is a bioinformatic program designed for the systematic identification of known antiphage defense mechanisms. The initial release of DefenseFinder v1.0.0 included 60 systems. Over the past three years, the number of antiphage systems incorporated into DefenseFinder has grown to 152. The increasing number of known systems makes it a challenge to enter the field and makes the interpretation of detections of antiphage systems difficult. Moreover, the rapid development of sequence-based predictions of structures offers novel possibilities of analysis and should be easily available. To overcome these challenges, we present a hub of resources on defense systems, including: 1) an updated version of DefenseFinder with a web-service search function, 2) a community-curated repository of knowledge on the systems, and 3) precomputed databases, which include annotations done on RefSeq genomes and structure predictions generated by AlphaFold. These pages can be freely accessed for users as a starting point on their journey to better understand a given system. We anticipate that these resources will foster the use of bioinformatics in the study of antiphage systems and will serve the community of researchers who study antiphage systems. This resource is available at: https://defensefinder.mdmlab.fr .
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- Authors
- Tesson, F., Planel, R., Egorov, A. A., Georjon, H., Vaysset, H., Brancotte, B., Néron, B., Mordret, E., Atkinson, G. C., Bernheim, A., & Cury, J.
- Affiliations
- Inserm (FR)
- Institut Pasteur (FR)
- Lund University (SE)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Cury, Jean
- ORCID
- Venue
- Peer Community Journal
- Publisher
- Peer Community In
- Published
- 2024-09-25
- Volume
- 4
- ISSN
- 2804-3871 (ISSN-L)
- OpenAlex
- W4402815517
- Cited by
- 120
- References
- 12
- Citations by year
- 2026: 52 · 2025: 52 · 2024: 16
- FWCI
- 32.92
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- cc-by
- Locations
- Peer Community Journal (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- HAL (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Funders
- Institut National de la Santé et de la Recherche Médicale (R21042KS/RSE22002KSA, R21042KS)
- National Science Council (2018-05973)
- Linköpings Universitet (2018-05973, 2022-06725)
- Knut och Alice Wallenbergs Stiftelse (2018-05973, 2020.0037)
- Kungliga Tekniska Högskolan (2018-05973)
- Vetenskapsrådet (2019-01085, 2023-02353, 05973, 2022-01603, 2018-, 201805973, 2022-06725)
- Fondation Bettencourt Schueller
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- phage resistance, CRISPR-Cas, phage immunity, web services, knowledge base, genome annotation, AlphaFold structure prediction, RefSeq genomes, bioinformatics resources
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