MacSyFinder v2: An improved search engine to model and identify molecular systems in genomes

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Néron, Bertrand | Denise, Rémi | Coluzzi, Charles | Touchon, Marie | Rocha, Eduardo | Abby, Sophie

Edité par CCSD -

International audience. Complex cellular functions are most often encoded by a set of genes rather than individualones. Furthermore, the genes in such “systems” are often encoded nearby in microbial genomes.MacSyFinder uses these properties to model and then accurately annotate cellular functions inmicrobial genomes at the system-level rather than at the individual-gene level. We hereby present amajor release of MacSyFinder [1], MacSyFinder version 2 (v2). This new version is coded inPython 3 (>= 3.7). The code was improved and rationalized to enable higher maintainability overtime. Several new features were added to allow more flexible modeling of the systems. Weintroduce a more intuitive and comprehensive search engine to identify all the best candidatesystems and sub-optimal ones that still respect the models’ constraints. We also present the novelmacsydata companion tool that enables the easy installation and broad distribution of the modelsdeveloped for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated,improved, and made available MacSyFinder popular models to this novel version: TXSScan andTFF-SF, CONJscan, and CasFinder. MacSyFinder v2 can be found at this URL:https://github.com/gem-pasteur/macsyfinderReferences1. Sophie S Abby, Bertrand Néron, Hervé Ménager, Marie Touchon, Eduardo PC Rocha. MacSyFinder: A Program toMine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLOS ONE,https://doi.org/10.1371/journal.pone.0110726, 2014.

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