StochasticContextFreeGrammars
A StochasticContextFreeGrammar is a stochastic generalisation of a context-free grammar. Introduced in natural language parsing, it is useful in working with RNA structure. Implementations in DART- Grammar object: DartSrc:scfg/paircfg.h
- Dynamic programming "fold envelopes" (iterators): DartSrc:scfg/foldenv.h
- Dynamic programming matrices (containers): DartSrc:scfg/paircfgdp.h
- Dowell RD, Eddy SR. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics. 2004 Jun 4;5:71.
- Holmes I. Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics. 2005 Mar 24;6:73.
- Rivas E. Evolutionary models for insertions and deletions in a probabilistic modeling framework. BMC Bioinformatics. 2005 Mar 21;6:63.
- Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 2004 Sep 24;32(16):4925-36. Print 2004.
- Rivas E, Eddy SR. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics. 2001;2:8. Epub 2001 Oct 10.
- Grate L, Herbster M, Hughey R, Haussler D, Mian IS, Noller H. RNA modeling using Gibbs sampling and stochastic context free grammars. Proc Int Conf Intell Syst Mol Biol. 1994;2:138-46.
- See also CovarianceModels
- Rzhetsky A, Fitch WM. Listening to viral tongues: comparing viral trees using a stochastic context-free grammar. Mol Biol Evol. 2005 Apr;22(4):905-13. Epub 2004 Dec 29.
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