Stochastic modeling of RNA pseudoknotted structures: a grammatical approach | Zendy

Liming Cai | Zendy; Russell L. Malmberg | Zendy; Yunzhou Wu | Zendy

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Stochastic modeling of RNA pseudoknotted structures: a grammatical approach

Author(s) -

Liming Cai,

Russell L. Malmberg,

Yunzhou Wu

Publication year - 2003

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btg1007

Subject(s) - synchronous context free grammar , stochastic context free grammar , computer science , grammar , rule based machine translation , context free grammar , grammar induction , computational linguistics , nucleic acid secondary structure , artificial intelligence , context (archaeology) , probabilistic logic , parsing , natural language processing , theoretical computer science , rna , tree adjoining grammar , biology , gene , paleontology , linguistics , philosophy , biochemistry , chemistry , example based machine translation

Modeling RNA pseudoknotted structures remains challenging. Methods have previously been developed to model RNA stem-loops successfully using stochastic context-free grammars (SCFG) adapted from computational linguistics; however, the additional complexity of pseudoknots has made modeling them more difficult. Formally a context-sensitive grammar is required, which would impose a large increase in complexity.

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