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This article is part of the supplement: Selected Proceedings of the 6th International Symposium on Bioinformatics Research and Applications (ISBRA'10)

Open Access Proceedings

Local structural alignment of RNA with affine gap model

Thomas King-Fung Wong*, Brenda Wing-Yan Cheung, Tak-Wah Lam and Siu-Ming Yiu*

Author Affiliations

Department of Computer Science, The University of Hong Kong, Hong Kong

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BMC Proceedings 2011, 5(Suppl 2):S2  doi:10.1186/1753-6561-5-S2-S2

Published: 28 April 2011



Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps.


In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem.


Based on an experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.