RNA secondary structure prediction and runtime optimization

1. Background RNA secondary structure Pseudoknots Non-coding RNA 2. CONTRAfold: Probabilistic RNA folding Overview of the algorithm Details of the algorithm Performance of CONTRAfold 3. Other RNA folding methods: Physics-based models and Stochastic Context Free Grammars Physics-based models Stochastic Context Free Grammars Advantages of CONTRAfold over these other approaches 4. How RNA folding is done from an algorithmic perspective The Nussinov folding algorithm A more elaborate algorithm 5. CandidateFold: RNA folding in O(n 2 ) time 6. Genome-wide “accessible” motif detection What is an RNA regulatory motif? What is an “accessible” motif? How do Wexler et al. detect regulatory motifs? Results obtained by applying the two-stage process