RNA Structure Prediction Including Pseudoknots Based on Stochastic Multiple Context-Free Grammar

@inproceedings{Kato2006RNASP,
  title={RNA Structure Prediction Including Pseudoknots Based on Stochastic Multiple Context-Free Grammar},
  author={Yuki Kato and Hiroyuki Seki and Tadao Kasami},
  year={2006}
}
Several grammars have been proposed for modeling RNA pseudoknotted structure. In this paper, we focus on multiple contextfree grammars (MCFGs), which are natural extension of context-free grammars and can represent pseudoknots, and extend a specific subclass of MCFGs to a probabilistic model called SMCFG. We present a polynomial time parsing algorithm for finding the most probable derivation tree and a probability parameter estimation method based on the EM algorithm. Furthermore, we show some… CONTINUE READING