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. 2022 May 10;13:2561. doi: 10.1038/s41467-022-30269-9

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a List of systems included in DefenseFinder. Systems are ordered alphabetically. For systems with several types, each system is represented by one type and other types are indicated in parentheses (Full list, Supplementary Data Table 1). b Workflow for the creation of DefenseFinder. c Example of a DefenseFinder rule (in the MacsyFinder syntax) for the detection of system CBASS type I. Cyclase and effector proteins are mandatory while the sensing protein is only accessory. This means the system allows for it to be missing in a detected CBASS type I system. Different profiles are recognized for a protein. ex cyclase (SMODS, AGC_C, Cycl100). d DefenseFinder function layout. DefenseFinder takes an ordered multifasta protein file. A search for specific HMM profiles is conducted, the MacSyfinder rules specific for antiviral systems are applied on the search results, generating three results files.