CoChat
Sign Up
PreprintCited by 120Bacteriophages and microbial interactionsCRISPR and Genetic EngineeringBacterial Genetics and Biotechnology

The DOI matches its Crossref record; its reference list is not available.

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

Open access
Tesson, Florian, Planel, Remi, Egorov, Artyom A, Georjon, Heloise, Vaysset, Hugo, Brancotte, Bryan, Neron, Bertrand, Mordret, Ernest, Atkinson, Gemma Catherine, Bernheim, Aude, Cury, Jean·2024·Peer Community Journal
DOI 10.1101/2024.01.25.577194

Preprint — published as 10.24072/pcjournal.470 · Paper page

Open this paper in CoChat — free account

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.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2024.01.25.577194

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

No citation lists for this paper

No citation lists for this paper yet — checked again daily.

References 59 · Cited by 120

Research works printed but not linked: 52

  1. 10.1038/s41579-023-00934-x · DOI
  2. 10.1146/annurev-genet-022120-112523 · DOI
  3. 10.1016/j.mib.2005.06.003 · DOI
  4. 10.1016/j.cell.2023.01.012 · DOI
  5. 10.1038/s41564-022-01162-4 · DOI
  6. 10.1038/s41467-020-16703-w · DOI
  7. 10.1016/j.cell.2023.07.020 · DOI
  8. 10.1016/j.molcel.2023.11.007 · DOI
  9. 10.1038/s41564-022-01158-0 · DOI
  10. 10.1016/j.molcel.2023.11.010 · DOI
  11. 10.1016/j.molcel.2021.10.020 · DOI
  12. 10.1128/JB.00904-06 · DOI
  13. 10.1126/science.abj8432 · DOI
  14. 10.1016/j.chom.2022.04.015 · DOI
  15. 10.1038/s41586-020-2762-2 · DOI
  16. 10.1126/science.abb1083 · DOI
  17. 10.1038/s41564-022-01157-1 · DOI
  18. 10.1101/2022.08.12.503731 · DOI
  19. 10.1101/2023.11.22.567924 · DOI
  20. 10.1016/j.mib.2022.102238 · DOI
  21. 10.1038/s41467-022-30269-9 · DOI
  22. 10.1016/j.mib.2005.06.006 · DOI
  23. 10.1016/j.molcel.2013.02.002 · DOI
  24. 10.1007/s00438-004-1048-y · DOI
  25. 10.1038/nmicrobiol.2017.72 · DOI
  26. 10.1128/mSystems.00534-20 · DOI
  27. 10.1016/j.mib.2023.102313 · DOI
  28. 10.1016/j.chom.2022.02.018 · DOI
  29. 10.1016/j.chom.2022.09.017 · DOI · Paper page
  30. 10.24072/pcjournal.250 · DOI
  31. 10.21105/joss.04296 · DOI
  32. 10.1093/nar/gkac247 · DOI
  33. 10.1038/s41587-023-01773-0 · DOI · Paper page
  34. 10.1534/genetics.110.121798 · DOI
  35. 10.1101/2021.09.27.462013 · DOI
  36. 10.1101/2023.05.28.542683 · DOI
  37. 10.1038/s41586-022-05444-z · DOI
  38. 10.1038/s41586-023-06855-2 · DOI · Paper page
  39. 10.1016/j.molcel.2022.09.008 · DOI · Paper page
  40. 10.1038/s41594-023-01172-8 · DOI
  41. 10.1126/science.ade2574 · DOI · Paper page
  42. 10.1038/s41467-022-28865-w · DOI · Paper page
  43. 10.1093/nar/gkac1077 · DOI
  44. 10.1093/nar/gkac1052 · DOI · Paper page
  45. 10.1093/nar/gkab314 · DOI · Paper page
  46. 10.7490/f1000research.1114334.1 · DOI
  47. 10.1101/2021.10.04.463034 · DOI · Paper page
  48. 10.1093/nar/gkv1189 · DOI · Paper page
  49. 10.1371/journal.pcbi.1002195 · DOI · Paper page
  50. 10.1093/nar/gkaa913 · DOI · Paper page
  51. 10.1186/1471-2105-10-421 · DOI · Paper page
  52. 10.1101/2022.09.02.506364 · DOI

Metadata

Authors
Tesson, F., Planel, R., Egorov, A. A., Georjon, H., Vaysset, H., Brancotte, B., Neron, B., Mordret, E., Atkinson, G. C., Bernheim, A., & Cury, J.
Affiliations
  • Inserm (FR)
  • Lund University (SE)
  • Centre National de la Recherche Scientifique (FR)
  • Institut Pasteur (FR)
Corresponding author
Cury, Jean
ORCID
Venue
Peer Community Journal
Publisher
openRxiv
Published
2024-01-26
Volume
4
ISSN
2804-3871 (ISSN-L)
DOI
10.1101/2024.01.25.577194
OpenAlex
W4402815517
Cited by
120
References
59
Citations by year
2026: 52 · 2025: 52 · 2024: 16
FWCI
32.92
Type
journal article
Language
en
Open access
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
  • Life Sciences › Immunology and Microbiology › Virology › 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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review