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ISMB
1994
13 years 6 months ago
RNA Modeling Using Gibbs Sampling and Stochastic Context Free Grammars
Leslie Grate, Mark Herbster, Richard Hughey, David...
CLEIEJ
2006
97views more  CLEIEJ 2006»
13 years 4 months ago
Prediction of RNA Pseudoknotted Secondary Structure using Stochastic Context Free Grammars (SCFG)
Pseudoknots are a frequent RNA structure that assumes essential roles for varied biocatalyst cell's functions. One of the most challenging fields in bioinformatics is the pre...
Rafael Garcia
LATA
2010
Springer
13 years 11 months ago
Extending Stochastic Context-Free Grammars for an Application in Bioinformatics
We extend stochastic context-free grammars such that the probability of applying a production can depend on the length of the subword that is generated from the application and sho...
Frank Weinberg, Markus E. Nebel
BMCBI
2005
99views more  BMCBI 2005»
13 years 4 months ago
Effective ambiguity checking in biosequence analysis
Background: Ambiguity is a problem in biosequence analysis that arises in various analysis tasks solved via dynamic programming, and in particular, in the modeling of families of ...
Janina Reeder, Peter Steffen, Robert Giegerich
IJBRA
2006
111views more  IJBRA 2006»
13 years 4 months ago
Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots
: Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches. Our previous work (Cai et al., 2003) in Stochastic Paral...
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Co...