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
RNA sequence analysis
Phylogenetic tree comparisons
- 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
- 03 Apr 2005
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