Parametrized Stochastic Grammars for RNA Secondary Structure Prediction

Details Parametrized Stochastic Grammars for RNA Secondary Structure Prediction Parametrized Stochastic Grammars for RNA Secondary Structure Prediction

2007-01-24

arxiv.org/abs/q-bio/0701036v1

Biology

Quantitative Biology

Biomolecules

5 pages, submitted to the 2007 Information Theory and Applications Workshop (ITA 2007)

Scientific paper

We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a posteriori estimation of the secondary structure of any new sequence in the family. The proposed SCFG architecture models RNA subsequences comprising paired bases as stochastically weighted Dyck-language words, i.e., as weighted balanced-parenthesis expressions. The length of each run of unpaired bases, forming a loop or a bulge, is taken to have a phase-type distribution: that of the hitting time in a finite-state Markov chain. Without loss of generality, each such Markov chain can be taken to have a bounded complexity. The scheme yields an overall family SCFG with a manageable number of parameters.

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