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A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databasesuse asterix (*) to get italics
F. Tesson, R. Planel, A. Egorov, H. Georjon, H. Vaysset, B. Brancotte, B. Néron, E. Mordret, A Bernheim, G. Atkinson, J. CuryPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
2024
<p>In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To<br>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.</p>
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defense systems; bacteria; phage; antiphage; genomic
NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).
Bacteria and archaea, Bioinformatics, Evolutionary genomics, Viruses and transposable elements
Brandon K. B. Seah, Max Emil Schön, Lopes Leão suggested: siroux1@gmail.com Simon Roux, Lopes Leão suggested: rafael.pinilla@bio.ku.dk Rafael Pinilla Redondo, Lopes Leão suggested: r.wheatley@qub.ac.uk Rachel Wheatley No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
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2024-04-17 18:30:32
Sishuo Wang