MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
| Autor: | Bertrand Néron, Eduardo Rocha, Rémi Denise, Marie Touchon, Sophie Abby, Charles Coluzzi |
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| Přispěvatelé: | Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University College Cork (UCC), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), EPCR lab acknowledges funding from the INCEPTION project (ANR-16-CONV-0005), Equipe FRM(Fondation pour la Recherche Médicale): EQU201903007835, and Laboratoire d’Excellence IBEIDIntegrative Biology of Emerging Infectious Diseases (ANR-10-LABX-62-IBEID). SSA received financial supportfrom the CNRS and TIMC lab (INSIS 'starting grant') and the French National Research Agency,'Investissements d’avenir' program ANR-15-IDEX-02, ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-15-IDEX-0002,UGA,IDEX UGA(2015) |
| Rok vydání: | 2023 |
| Předmět: | |
| Zdroj: | Peer Community Journal Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩ |
| ISSN: | 2804-3871 |
| DOI: | 10.24072/pcjournal.250 |
| Popis: | Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models' constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models. |
| Databáze: | OpenAIRE |
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