Specific papers of interest
Michael Brown and Charles Wilson.
Pseudoknot Modeling Using Intersections of Stochastic
Context Free Grammars with Applications to Database Search
A model based on intersections of stochastic context free
grammars is presented to allow for the modeling of RNA
pseudoknot structures. The model runs relatively fast, having
the same order running time as stochastic context free grammar parsers.
The model is shown to be able to perform database searches and
find RNA sequences which resemble RNA pseudoknots which bind
biotin. The problem domain of RNA biotin binders has significance
in the support of the RNA world model of early life on earth.
computational biology research at UCSC for more interesting papers.
Baskin Center for Computer Engineering and Information Sciences
University of California, Santa Cruz