A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
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 prog...
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2024-09-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.470/ |
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| author | Tesson, Florian Planel, Rémi Egorov, Artyom A Georjon, Héloïse Vaysset, Hugo Brancotte, Bryan Néron, Bertrand Mordret, Ernest Atkinson, Gemma Catherine Bernheim, Aude Cury, Jean |
| author_facet | Tesson, Florian Planel, Rémi Egorov, Artyom A Georjon, Héloïse Vaysset, Hugo Brancotte, Bryan Néron, Bertrand Mordret, Ernest Atkinson, Gemma Catherine Bernheim, Aude Cury, Jean |
| author_sort | Tesson, Florian |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-4139f73f1d79452d954c4c0cd7d26844 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2024-09-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-4139f73f1d79452d954c4c0cd7d268442025-02-07T10:17:17ZengPeer Community InPeer Community Journal2804-38712024-09-01410.24072/pcjournal.47010.24072/pcjournal.470A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases Tesson, Florian0https://orcid.org/0000-0003-4038-1154Planel, Rémi1https://orcid.org/0000-0002-7826-3316Egorov, Artyom A2https://orcid.org/0000-0001-5578-5384Georjon, Héloïse3https://orcid.org/0000-0003-0694-542XVaysset, Hugo4https://orcid.org/0009-0007-3134-1966Brancotte, Bryan5https://orcid.org/0000-0001-8669-5525Néron, Bertrand6https://orcid.org/0000-0002-0220-0482Mordret, Ernest7https://orcid.org/0000-0001-6641-8336Atkinson, Gemma Catherine8https://orcid.org/0000-0002-4861-4584Bernheim, Aude9https://orcid.org/0000-0003-0212-777XCury, Jean10https://orcid.org/0000-0002-6462-8783Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes lab, 75015, Paris, France; Université Paris Cité, INSERM, IAME, 75018 Paris, FranceInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, FranceDepartment of Experimental Medical Science, and Lund University Virus Centre, Lund University, 221 00 Lund, SwedenInstitut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes lab, 75015, Paris, FranceInstitut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes lab, 75015, Paris, France; Institut Curie, Université PSL, Sorbonne Université, CNRS, Laboratoire Physico Chimie Curie, UMR 168, 75005 Paris, France; AgroParisTech, 91120, Palaiseau, FranceInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, FranceInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, FranceInstitut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes lab, 75015, Paris, FranceDepartment of Experimental Medical Science, and Lund University Virus Centre, Lund University, 221 00 Lund, SwedenInstitut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes lab, 75015, Paris, FranceInstitut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes lab, 75015, Paris, FranceIn 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.https://peercommunityjournal.org/articles/10.24072/pcjournal.470/Defense Systems, Phage, Antiphage, Bacteria, Bioinformatics |
| spellingShingle | Tesson, Florian Planel, Rémi Egorov, Artyom A Georjon, Héloïse Vaysset, Hugo Brancotte, Bryan Néron, Bertrand Mordret, Ernest Atkinson, Gemma Catherine Bernheim, Aude Cury, Jean A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases Peer Community Journal Defense Systems, Phage, Antiphage, Bacteria, Bioinformatics |
| title | A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
|
| title_full | A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
|
| title_fullStr | A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
|
| title_full_unstemmed | A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
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| title_short | A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases
|
| title_sort | comprehensive resource for exploring antiphage defense defensefinder webservice wiki and databases |
| topic | Defense Systems, Phage, Antiphage, Bacteria, Bioinformatics |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.470/ |
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