Section: Genomics
Topic: Genetics/Genomics

MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Néron, Bertrand1 ; Denise, Rémi2, 3 ; Coluzzi, Charles2 ; Touchon, Marie2 ; Rocha, Eduardo P.C.2  ; Abby, Sophie S.4  
1 Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
2 Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
3 APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
4 Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France

Corresponding author(s): Rocha, Eduardo P.C. (erocha@pasteur.fr); Abby, Sophie S. (sophie.abby@univ-grenoble-alpes.fr)

10.24072/pcjournal.250 - Peer Community Journal, Volume 3 (2023), article no. e28.

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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.

Published online:
DOI: 10.24072/pcjournal.250
Type: Software tool
Mots-clés : genome annotation; modelling; comparative genomics; prokaryotes; microbiology; functional annotation; bioinformatics

Néron, Bertrand 1; Denise, Rémi 2, 3; Coluzzi, Charles 2; Touchon, Marie 2; Rocha, Eduardo P.C. 2; Abby, Sophie S. 4

1 Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
2 Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
3 APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
4 Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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     title = {MacSyFinder v2: {Improved} modelling and search engine to identify molecular systems in genomes},
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Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Peer Community Journal, Volume 3 (2023), article  no. e28. doi : 10.24072/pcjournal.250. https://peercommunityjournal.org/articles/10.24072/pcjournal.250/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.genomics.100233

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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