Représentation et recherche de motifs cycliques et structuraux d’ARN connus dans les structures secondaires
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are polymers of nucleotides essential for the survival of the cell.  Contrary to DNA, whose main role is to store genetic information, RNA is involved in multiple metabolic processes.  For example, RNA is involved in the transfer of information from DNA to protein, the processing and modification of other RNAs, the regulation of gene expression, the end-maintenance of chromosomes, and the sorting of proteins within the cell.  This functional versatility of RNA comes from its structural diversity.  Our laboratory developed MC-Fold, an algorithm that predicts RNA structures by representing them with nucleotide interaction graphs.  The nodes in these graphs represent the nucleotides, and the edges the interactions between them.  Our laboratory also observed that a limited number of interaction cycles can define the structure of any RNA motif.  The formation of these cycles is determined by the nucleotide sequence and MC-Fold determines the most likely cycles based on that sequence.   In this Master Degree project, I first built a database of structural and functional RNA motifs, bdMotifs, based on their constituent cycles.  Then, I implemented an algorithm, MC-Motifs, which detects motifs within interaction graphs generated either by MC-Fold or by any other method.  Finally, I validated my algorithm on known RNA structures such as the 5S, 16S and 23S ribosomal RNA (rRNA) and predicted structure of riboswitches.   The Master thesis is divided into five chapters.  The first chapter presents the chemical structure of RNA, its cellular functions and the structural folding of the polymer.  In the second chapter, the database bdMotifs is described.  In the third chapter, the MC-Motifs algorithm is introduced.  In the fourth chapter, I present the results of MC-Motifs.  Finally, in the last chapter, I discuss theses results and I give a conclusion on the project.
Motif Cycle RNA Secondary structure