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- Title
Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
- Authors
Matsui, Hiroshi; Sato, Kengo; Sakakibara, Yasubumi
- Abstract
Since the whole genome sequences of many species have been determined, computational prediction of RNA secondary structures and computational identification of those non-coding RNA regions by comparative genomics become important. Therefore, more advanced alignment methods are required. Recently, an approach of structural alignment for RNA sequences has been introduced to solve these problems. Pair hidden Markov models on tree structures (PHMMTSs) proposed by Sakakibara are efficient automata-theoretic models for structural alignment of RNA secondary structures, although PHMMTSs are incapable of handling pseudoknots. On the other hand, tree adjoining grammars (TAGs), a subclass of context-sensitive grammars, are suitable for modeling pseudoknots. Our goal is to extend PHMMTSs by incorporating TAGs to be able to handle pseudoknots.
- Publication
Bioinformatics (Oxford, England), 2005, Vol 21, Issue 11, p2611
- ISSN
1367-4803
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/bti385