Section: Contracts and Grants with Industry
RNA-RECOD , ANR BLANC 2006-2010: Influence of mRNA structures on ribosome accuracy . Normal decoding could be diverted by sequences and structures on the mRNA and led to recoding. Analysing these variations constitutes a powerful tool to understand the normal curse of action of the translational machinery. The four teams involved in the project develop complementary approaches that have previously allowed the identification of several elements involved in recoding. Very recently, using a cryo-eletromicroscopy approach, we deciphered for the first time the precise role of the pseudoknot in a -1 frameshifting event. The project gathers together several complementary approaches including biochemistry, genetics, molecular and structural biology and bioinformatics. The goal of the study is to i) compare the molecular mechanisms involved in several recoding events (-1 and +1 frameshifting, pyrrolysine incorporation), focusing on the associated structural modifications and ii) identify new recoding sites in genomes.
AMIS-ARN , ANR BLANC 2009-2012: Graph Algorithms and Automatic Softwares for Interactive RNA Structure Modelling . We aim to do substantial progress in the problem of automatically or semi-automatically modelling the three-dimensional structure of RNA molecules, given their sequence. By semi-automatically we mean developing algorithms and software that can automatically propose (good) solutions, and that can efficiently compute alternative solutions according to some new constraints or some new hypotheses given by the expert modeler. More precisely, we plan to work on the three following points: 1.Development of computational methods for solving some key steps necessary for modelling RNA 3D structures. These methods will rely on new graph algorithms for molecular structures and on biological expertise on sequence-structure relations in RNA molecules. 2.Implemention of these methods in a software suite, Paradise , which is being developed by one of the partners (E. Westhof's lab, Strasbourg University) and which will be made freely available to the scientific community. 3. Application of these methods in order to model several molecules of interest.
Lri and Inra-Mig are partners in a one-year regional project Afon : Annotation FONctionnelle (Functional Annotation) . The aim of the project is to design semi-automatic methods to help scientists in the task of functional annotation of prokaryotic genomes.