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Master thesis

Développement d'un outil de recherche automatisée des éléments génétiques mobiles de type ICE dans les génomes bactériens (ICE-Finder)

Abstract : ICE ("integrative conjugating elements") and IME ("integrative mobilizable elements") are important elements of horizontal gene transfer. Today, there are methods to detect mobile genetic elements but none is specialized in the research of ICE or IME. This training was conducted in a collaborative project to create a computerized and automated method for the detection of ICE and IME in bacterial genomes. The methodology is based on identifying and positioning in the genomes of three classes of genes encoding proteins which are specific of these elements (coupling protein, relaxase , integrase) and development of a database gathering data on these genes. During the study, a prototype program (ICEFinder) for automatic search of ICE / IME has been developed to perform the following tasks: (1) Detect the genes encoding the proteins of interest in bacterial genomes (2) Locate the genes on the genome (3) Search and locate potential terminals ICE / IME (4) Get the gene content of these mobile genetic elements The execution of this program on the whole genomes of streptococci has been used to characterize and limit 109 ICE / IME in 49 of the 72 genomes studied.
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Master thesis
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http://docnum.univ-lorraine.fr/public/BUS_M_2013_AUBERT_YANN.pdf
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https://hal.univ-lorraine.fr/hal-01866115
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Yann Aubert. Développement d'un outil de recherche automatisée des éléments génétiques mobiles de type ICE dans les génomes bactériens (ICE-Finder). Microbiologie et Parasitologie. 2013. ⟨hal-01866115⟩

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