Tree adjoining grammars for RNA structure prediction

Yasuo Uemura, Aki Hasegawa, Satoshi Kobayashi, Takashi Yokomori

Research output: Contribution to journalArticle

128 Citations (Scopus)

Abstract

In this paper, we are concerned with identifying a subclass of tree adjoining grammars (TAGs) that is suitable for the application to modeling and predicting RNA secondary structures. The goal of this paper is twofold: For the purpose of applying to the RNA secondary structure prediction problem, we first introduce a special subclass of TAGs and develop a fast parsing algorithm for the subclass, together with some of its language theoretic characterizations. Then, based on the algorithm, we develop a prediction system and demonstrate the effectiveness of the system by presenting some experimental results obtained from biological data, where free energy evaluation selection for parse trees is incorporated into the algorithm.

Original languageEnglish
Pages (from-to)277-303
Number of pages27
JournalTheoretical Computer Science
Volume210
Issue number2
Publication statusPublished - 1999 Jan 17
Externally publishedYes

Fingerprint

Structure Prediction
RNA
Grammar
RNA Secondary Structure
Parsing
Free energy
Free Energy
Prediction
Evaluation
Experimental Results
Modeling
Demonstrate

Keywords

  • Parsing algorithms
  • RNA secondary structures
  • RNA structure prediction
  • Tree adjoining grammars

ASJC Scopus subject areas

  • Computational Theory and Mathematics

Cite this

Uemura, Y., Hasegawa, A., Kobayashi, S., & Yokomori, T. (1999). Tree adjoining grammars for RNA structure prediction. Theoretical Computer Science, 210(2), 277-303.

Tree adjoining grammars for RNA structure prediction. / Uemura, Yasuo; Hasegawa, Aki; Kobayashi, Satoshi; Yokomori, Takashi.

In: Theoretical Computer Science, Vol. 210, No. 2, 17.01.1999, p. 277-303.

Research output: Contribution to journalArticle

Uemura, Y, Hasegawa, A, Kobayashi, S & Yokomori, T 1999, 'Tree adjoining grammars for RNA structure prediction', Theoretical Computer Science, vol. 210, no. 2, pp. 277-303.
Uemura Y, Hasegawa A, Kobayashi S, Yokomori T. Tree adjoining grammars for RNA structure prediction. Theoretical Computer Science. 1999 Jan 17;210(2):277-303.
Uemura, Yasuo ; Hasegawa, Aki ; Kobayashi, Satoshi ; Yokomori, Takashi. / Tree adjoining grammars for RNA structure prediction. In: Theoretical Computer Science. 1999 ; Vol. 210, No. 2. pp. 277-303.
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