Recherche des sites de régulation de la transcription dans des génomes bactériens

Abstract : Many programs have been developed to identify transcription factor binding sites. Most of them are not able to infer two-word motifs with variable spacer lengths, characteristics of RNA polymerase Sigma (s) Factor Binding Sites (SFBSs). The aim of this thesis is to design an algorithm taking into account the biological structural observations about these sites, in order to their relevant prediction. We describe a new approach, SIGffRid (SIGma Factor binding sites Finder using R?MES to select Input Data), to identify SFBSs by comparing two related bacterial genomes. The method performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and -10 boxes. These patterns are then grouped using pairs of short seeds, allowing a variable-length spacer between them. This is followed by motif extension guided by statistical considerations. Finally, statitically feasible and relevant motifs are selected. We applied our method to the pair of related bacterial genomes of Streptomyces coelicolor A3(2) and Streptomyces avermitilis. We demonstrate that our approach combining statistical and biological criteria was successful to predict SFBSs, and envisage ameliorations.
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Theses
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http://docnum.univ-lorraine.fr/prive/SCD_T_2007_0097_TOUZAIN.pdf
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https://hal.univ-lorraine.fr/tel-01748231
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Submitted on : Thursday, March 29, 2018 - 11:29:14 AM
Last modification on : Tuesday, April 24, 2018 - 1:30:20 PM

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Fabrice Touzain. Recherche des sites de régulation de la transcription dans des génomes bactériens. Autre [cs.OH]. Université Henri Poincaré - Nancy 1, 2007. Français. ⟨NNT : 2007NAN10097⟩. ⟨tel-01748231⟩

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