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Updated: Mar 24, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
A comprehensive study of RNA secondary structure alignment algorithms
Jimmy Ka Ho Chiu1, Yi-Ping Phoebe Chen1
1Department of Computer Science and Information Technology, La Trobe University, Melbourne, Victoria, Australia.
Abstract:
RNA secondary structure alignment has received more attention since the discovery of the structure-function relationships in some non-protein-encoding RNAs. However, unlike the pure sequence alignment problem, which has been solved in polynomial time, secondary structure alignment incorporates the base pairings as another information dimension in addition to the base sequence. This problem therefore becomes more challenging. In this study, we classify the selected approaches, and algorithmically illustrate how these methods address the alignment problems with different structure types. Other features such as the types of base pair edit operations supported and the time complexity are also compared.
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