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Book Sections Year : 2019

Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan

Abstract

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.
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Dates and versions

pasteur-02867882 , version 1 (16-06-2020)

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Jean Cury, Sophie S. Abby, Olivia Doppelt-Azeroual, Bertrand Néron, Eduardo P C Rocha. Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan. 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⟩. ⟨pasteur-02867882⟩
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