Tree adjoining grammars for RNA structure prediction
Theoretical Computer Science - Special issue: Genome informatics
Pseudoknots in RNA secondary structures
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
Classifying RNA pseudoknotted structures
Theoretical Computer Science
Searching Genomes for Noncoding RNA Using FastR
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The structures of non-coding RNAs are found to be critical in many biological functions. In particular, pseudoknotted structures play an important role in some of these functions. Different pseudoknotted structures may have different functionalities. Algorithms developed to handle pseudoknotted ncRNAs are usually designed for specific pseudoknot structures (e.g. structural alignment algorithms). It is desirable to have a tool to classify a given RNA secondary structure into different types. In this paper, we solve this problem by providing a set of efficient algorithms to perform the classification. We implemented the algorithms and used them in the web-based tool RNASAlign (http://www.bio8.cs.hku.hk/RNASAlign) which can automatically classify the input structure into the correct type, then perform the structural alignment according to the identified type. The classification algorithms proposed in the paper are found to be effective.