MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
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 integra...
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| Format: | Article |
| Language: | English |
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Peer Community In
2023-03-01
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| Series: | Peer Community Journal |
| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.250/ |
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| author | Néron, Bertrand Denise, Rémi Coluzzi, Charles Touchon, Marie Rocha, Eduardo P.C. Abby, Sophie S. |
| author_facet | Néron, Bertrand Denise, Rémi Coluzzi, Charles Touchon, Marie Rocha, Eduardo P.C. Abby, Sophie S. |
| author_sort | Néron, Bertrand |
| collection | DOAJ |
| description | 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.
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| format | Article |
| id | doaj-art-2ebc353f03c54ff8997e747060c25dbd |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2023-03-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-2ebc353f03c54ff8997e747060c25dbd2025-02-07T10:16:49ZengPeer Community InPeer Community Journal2804-38712023-03-01310.24072/pcjournal.25010.24072/pcjournal.250MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes Néron, Bertrand0https://orcid.org/0000-0002-0220-0482Denise, Rémi1https://orcid.org/0000-0003-2277-689XColuzzi, Charles2https://orcid.org/0000-0003-2238-0836Touchon, Marie3https://orcid.org/0000-0001-7389-447XRocha, Eduardo P.C.4https://orcid.org/0000-0001-7704-822XAbby, Sophie S.5https://orcid.org/0000-0002-5231-3346Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France; APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, IrelandInstitut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, FranceUniv. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, FranceComplex 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. https://peercommunityjournal.org/articles/10.24072/pcjournal.250/ |
| spellingShingle | 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 |
| title | MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
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| title_full | MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
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| title_fullStr | MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
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| title_full_unstemmed | MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
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| title_short | MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
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| title_sort | macsyfinder v2 improved modelling and search engine to identify molecular systems in genomes |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.250/ |
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