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Title: Stochastic multiple context-free grammar for RNA pseudoknot modeling
Authors: Kato, Yuki
Seki, Hiroyuki
カトウ, ユウキ
セキ, ヒロユキ
加藤, 有己
関, 浩之
Issue Date: Mar-2006
Publisher: Nara Institute of Science and Technology
Series/Report no.: Information Science Technical Report ~ TR2006002
Abstract: Several formal grammars have been proposed for modeling RNA secondary structure including substructure called pseudoknot. In this paper, we focus on multiple context-free grammars (MCFGs), which are natural extension of context-free grammars and can represent pseudoknots, and extend a specific subclass of MCFGs to a probabilistic model called a stochastic MCFG (SMCFG). We design a polynomial time parsing algorithm for finding the most probable derivation tree and a probability parameter estimation method based on the EM (expectation maximization) algorithm. Also, we show some experimental results of RNA secondary structure prediction with pseudoknots using SMCFG algorithm.
ISSN: 0919-9527
Text Version: author
Appears in Collections:テクニカルレポート / Technical Report

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