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Section: Genomics
Topic:
Genetics/Genomics
MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
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.
Type: Software tool
Néron, Bertrand 1; Denise, Rémi 2, 3; Coluzzi, Charles 2; Touchon, Marie 2; Rocha, Eduardo P.C. 2; Abby, Sophie S. 4
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@article{10_24072_pcjournal_250, author = {N\'eron, Bertrand and Denise, R\'emi and Coluzzi, Charles and Touchon, Marie and Rocha, Eduardo P.C. and Abby, Sophie S.}, title = {MacSyFinder v2: {Improved} modelling and search engine to identify molecular systems in genomes}, journal = {Peer Community Journal}, eid = {e28}, publisher = {Peer Community In}, volume = {3}, year = {2023}, doi = {10.24072/pcjournal.250}, url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.250/} }
TY - JOUR AU - Néron, Bertrand AU - Denise, Rémi AU - Coluzzi, Charles AU - Touchon, Marie AU - Rocha, Eduardo P.C. AU - Abby, Sophie S. TI - MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes JO - Peer Community Journal PY - 2023 VL - 3 PB - Peer Community In UR - https://peercommunityjournal.org/articles/10.24072/pcjournal.250/ DO - 10.24072/pcjournal.250 ID - 10_24072_pcjournal_250 ER -
%0 Journal Article %A Néron, Bertrand %A Denise, Rémi %A Coluzzi, Charles %A Touchon, Marie %A Rocha, Eduardo P.C. %A Abby, Sophie S. %T MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes %J Peer Community Journal %D 2023 %V 3 %I Peer Community In %U https://peercommunityjournal.org/articles/10.24072/pcjournal.250/ %R 10.24072/pcjournal.250 %F 10_24072_pcjournal_250
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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