IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella

Autor: Bertrand Néron, Eloi Littner, Matthieu Haudiquet, Amandine Perrin, Jean Cury, Eduardo P. C. Rocha

Publikováno v: Microorganisms, Vol 10, Iss 4, p 700 (2022)

Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance

Externí odkaz: https://doaj.org/article/60d097f8e95e40d780b8b6111baca133

BioConvert: a comprehensive format converter for life sciences

Autor: Hugo Caro, Sulyvan Dollin, Anne Biton, Bryan Brancotte, Dimitri Desvillechabrol, Yoann Dufresne, Blaise Li, Etienne Kornobis, Frédéric Lemoine, Nicolas Maillet, Amandine Perrin, Nicolas Traut, Bertrand Néron, Thomas Cokelaer

Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They consta

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a7a2cefc8b4c2ab1f4662fb4c9d396e
https://doi.org/10.1101/2023.03.13.532455

MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

Autor: Sophie S Abby, Bertrand Néron, Hervé Ménager, Marie Touchon, Eduardo P C Rocha

Publikováno v: PLoS ONE, Vol 9, Iss 10, p e110726 (2014)

Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder) provides a flexible fr

Externí odkaz: https://doaj.org/article/341dd8e3a2484b6d9b52d410e218afb7

Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan

Autor: Olivia Doppelt-Azeroual, Bertrand Néron, Eduardo P. C. Rocha, Sophie S. Abby, Jean Cury

Publikováno v: Horizontal Gene Transfer ISBN: 9781493998760
Horizontal Gene Transfer : Methods and Protocols
Fernando de la Cruz. Horizontal Gene Transfer : Methods and Protocols, Springer Science; Business Media, pp.265-283, 2019, 978-1-4939-9876-0. ⟨10.1007/978-1-4939-9877-7_19⟩

Part of the Methods in Molecular Biology book series (MIMB, volume 2075); International audience; We present a computational method to identify conjugative systems in plasmids and chromosomes using the CONJscan module of MacSyFinder. The method relie

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::673d846850721990a8f1bc58ebfbae58
https://doi.org/10.1007/978-1-4939-9877-7_19

Identification of protein secretion systems in bacterial genomes

Autor: Sophie S. Abby, Marie Touchon, Jean Cury, Eduardo P. C. Rocha, Julien Guglielmini, Bertrand Néron

Publikováno v: Scientific Reports
Scientific Reports, 2016, 6, ⟨10.1038/srep23080⟩
Scientific Reports, Nature Publishing Group, 2016, 6, ⟨10.1038/srep23080⟩

Bacteria with two cell membranes (diderms) have evolved complex systems for protein secretion. These systems were extensively studied in some model bacteria, but the characterisation of their diversity has lagged behind due to lack of standard annota

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ebdb9b318f73d0d61587cfe44dc4953f
https://hal-pasteur.archives-ouvertes.fr/pasteur-01374967