Summary
We present an RNA representation scheme in which an RNA structure is described as a sequence of units, each of which stands for either an unpaired base or a base pair in the RNA molecule. With this structural representation scheme, we give efficient algorithms for computing the distance and alignment between two RNA secondary structures based on edit operations and on the assumptions in which either no bond-breaking operation is allowed or bond-breaking activities are considered. The techniques provide a foundation for developing solutions to the hard problems concerning RNA tertiary structure comparisons. Some experimental results based on real-world RNA data are also reported.
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© 2005 Springer-Verlag London Limited
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Zhang, K. (2005). RNA Structure Comparison and Alignment. In: Wu, X., Jain, L., Wang, J.T., Zaki, M.J., Toivonen, H.T., Shasha, D. (eds) Data Mining in Bioinformatics. Advanced Information and Knowledge Processing. Springer, London. https://doi.org/10.1007/1-84628-059-1_4
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DOI: https://doi.org/10.1007/1-84628-059-1_4
Publisher Name: Springer, London
Print ISBN: 978-1-85233-671-4
Online ISBN: 978-1-84628-059-7
eBook Packages: Computer ScienceComputer Science (R0)