Stochastic Regular Approximation of Tree Grammars and Its Application to Faster ncRNA Family Annotation

Kazuya Ogasawara, Satoshi Kobayashi
2007 IPSJ Digital Courier  
Tree Adjoining Grammar (TAG) is a useful grammatical tool to model RNA secondary structures containing pseudoknots, but its time complexity for parsing is not small enough for the practical use. Recently, Weinberg and Ruzzo proposed a method of approximating stochastic context free grammar by stochastic regular grammar and applied it to faster genome annotation of non-coding RNA families. This paper proposes a method for extending their idea to stochastic approximation of TAGs by regular
more » ... s. We will also report some preliminary experimental results on how well we can filter out non candidate parts of genome sequences by using obtained approximate regular grammars. * G t, t does not contain a node with OA constraint and t 0 ∈ C. }
doi:10.2197/ipsjdc.3.746 fatcat:5hpy3aoryvay5ketu6m4lqosny