Stochastic context-free grammar

A very nice general tutorial of HMMs is given in (Rabiner, 1989). An extension of HMMs from finite automata (which is the deterministic version of a Markov chain) to context-free languages leads to the concept of a stochastic context-free grammar. Such grammars have been used in an analogous way to predict RNA secondary structures (Grate et al., 1994). 

Knudsen, B. and Hein, J. (2003) Pfold RNA secondary structure prediction using stochastic context-free grammars. Nucl. Acids Res. 31, 3423-3428. 

Sakakibara, Y. Brown, M. Hughey, R. Mian, I.S. Sjblander, K. Underwood, R.C. Haussler, D. (1994). Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res., Vol. 22, pp. 5112-5120. 

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