Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan
| Autor: | Olivia Doppelt-Azeroual, Bertrand Néron, Eduardo P. C. Rocha, Sophie S. Abby, Jean Cury |
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| Přispěvatelé: | Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génomique et Évolution des Microorganismes (TIMC-IMAG-GEM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 [2016-2019] (UGA [2016-2019]), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, This work was supported by the ANR MAGISBAC project [ANR-14-CE10-0007], the CNRS, and the Institut Pasteur., Fernando de la Cruz, We thank the collaborators who have worked with us on this topic in the last decade, notably Fernando de la Cruz, Chris Smillie, Marie Touchon, Maria Pilar Garcillan-Barcia, and Julien Guglielmini., ANR-14-CE10-0007,MAGISBAC,Génèse et maintenance des chromosomes secondaire bactériens(2014), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS) |
| Rok vydání: | 2019 |
| Předmět: |
Comparative genomics
0303 health sciences biology Conjugation Integrative conjugative element 030306 microbiology Computer science [SDV]Life Sciences [q-bio] Chromosome Bacterial genome size Computational biology Plasmid [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology Integrase 03 medical and health sciences Identification (information) biology.protein Genomic islands [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] Mobile genetic elements Protein profiles Comparative genomics Integrase MacSyFinder 030304 developmental biology |
| Zdroj: | 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⟩ |
| DOI: | 10.1007/978-1-4939-9877-7_19 |
| Popis: | 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 relies on the identification of the protein components of the system using hidden Markov model profiles and then checking that the composition and genetic organization of the system is consistent with that expected from a conjugative system. The method can be assessed online using the Galaxy workflow or locally using a standalone software. The latter version allows to modify the models of the module (i.e., to change the expected components, their number, and their organization).CONJscan identifies conjugative systems, but when the mobile genetic element is integrative (ICE), one often also wants to delimit it from the chromosome. We present a method, with a script, to use the results of CONJscan and comparative genomics to delimit ICE in chromosomes. The method provides a visual representation of the ICE location. Together, these methods facilitate the identification of conjugative elements in bacterial genomes. |
| Databáze: | OpenAIRE |
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