The study of RNA kinetics is arguably the next frontier in RNA bioinformatics. It offers a much more faithful picture of the folding process than traditional approaches based on energy-minimization or thermodynamic equilibrium. However, the development of acurate and computationally efficient bioinformatics methods for RNA kinetics is challenged by the scarcity of available data as well as the computational intractability of some of its subtasks.
The goal of the RNALands project is to overcome those difficulties by gathering a consortium of experts in RNA bioinformatics, genomics and combinatorics. These experts will work in tight collaboration over the 2015-2018 period on some of the key issues in RNA kinetics, and will:
- Gather and annotate a comprehensive collection of biological examples and applications to serve as golden-standard for benchmarking computational tools;
- Design efficient computational methods to generate simplified and representative folding landscapes, thereby overcoming the difficulties encountered by traditional approaches for RNA kinetics and paving the way for scalable methods;
- Explore preexisting and novel heuristics to estimate energy barriers to effectively derive realistic refolding rates for exact and approximated coarse grained landscapes;
- Provide analysis tools for analyzing folding kinetics as Markov processes on coarse grain landscapes, either based on numerical integration or model-checking, thus enabling fast and accurate predictions;
- Extend and adapt these methods for a study of co-transcriptional folding and other changing landscapes to amount for the analysis of biological paradigms not treatable by existing approaches.