A Comprehensive Resource for Exploring Antiphage Defense : DefenseFinder Webservice,Wiki and Databases
Tesson, Florian ; Planel, Rémi ; Egorov, Artyom A. ; Georjon, Héloïse ; Vaysset, Hugo ; Brancotte, Bryan ; Néron, Bertrand ; Mordret, Ernest ; Atkinson, Gemma Catherine LU
and Bernheim, Aude
, et al.
(2024)
In Peer Community Journal
4.
- 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). De-fenseFinder is a bioinformatic program designed for the systematic identification of known antiphage defense mechanisms. The initial release of DefenseFinder v1.0.0 included 60 sys-tems. Over the past three years, the number of antiphage systems incorporated into De-fenseFinder has grown to 152. The increasing number of known systems makes it a chal-lenge to enter the field and makes the interpretation of detections of antiphage systems difficult. Moreover, the rapid... (More)
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). De-fenseFinder is a bioinformatic program designed for the systematic identification of known antiphage defense mechanisms. The initial release of DefenseFinder v1.0.0 included 60 sys-tems. Over the past three years, the number of antiphage systems incorporated into De-fenseFinder has grown to 152. The increasing number of known systems makes it a chal-lenge to enter the field and makes the interpretation of detections of antiphage systems difficult. Moreover, the rapid development of sequence-based predictions of structures of-fers novel possibilities of analysis and should be easily available. To overcome these chal-lenges, 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 sys-tem. 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.
(Less)
- author
- Tesson, Florian
; Planel, Rémi
; Egorov, Artyom A.
; Georjon, Héloïse
; Vaysset, Hugo
; Brancotte, Bryan
; Néron, Bertrand
; Mordret, Ernest
; Atkinson, Gemma Catherine
LU
and Bernheim, Aude
, et al. (More)
- Tesson, Florian
; Planel, Rémi
; Egorov, Artyom A.
; Georjon, Héloïse
; Vaysset, Hugo
; Brancotte, Bryan
; Néron, Bertrand
; Mordret, Ernest
; Atkinson, Gemma Catherine
LU
; Bernheim, Aude
and Cury, Jean
(Less)
- organization
- publishing date
- 2024
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- antiphage, bacteria, defense systems, genomic, phage
- in
- Peer Community Journal
- volume
- 4
- article number
- e91
- publisher
- Peer Community in
- external identifiers
-
- scopus:85205917701
- ISSN
- 2804-3871
- DOI
- 10.24072/pcjournal.470
- language
- English
- LU publication?
- yes
- id
- 99bee894-09da-4c60-a61c-9c89f36e898f
- date added to LUP
- 2024-12-20 10:01:44
- date last changed
- 2025-05-23 09:50:09
@article{99bee894-09da-4c60-a61c-9c89f36e898f,
abstract = {{<p>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). De-fenseFinder is a bioinformatic program designed for the systematic identification of known antiphage defense mechanisms. The initial release of DefenseFinder v1.0.0 included 60 sys-tems. Over the past three years, the number of antiphage systems incorporated into De-fenseFinder has grown to 152. The increasing number of known systems makes it a chal-lenge to enter the field and makes the interpretation of detections of antiphage systems difficult. Moreover, the rapid development of sequence-based predictions of structures of-fers novel possibilities of analysis and should be easily available. To overcome these chal-lenges, 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 sys-tem. 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.</p>}},
author = {{Tesson, Florian and Planel, Rémi and Egorov, Artyom A. and Georjon, Héloïse and Vaysset, Hugo and Brancotte, Bryan and Néron, Bertrand and Mordret, Ernest and Atkinson, Gemma Catherine and Bernheim, Aude and Cury, Jean}},
issn = {{2804-3871}},
keywords = {{antiphage; bacteria; defense systems; genomic; phage}},
language = {{eng}},
publisher = {{Peer Community in}},
series = {{Peer Community Journal}},
title = {{A Comprehensive Resource for Exploring Antiphage Defense : DefenseFinder Webservice,Wiki and Databases}},
url = {{http://dx.doi.org/10.24072/pcjournal.470}},
doi = {{10.24072/pcjournal.470}},
volume = {{4}},
year = {{2024}},
}