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Title: Structural alignment of RNA with complex pseudoknot structure
Authors: Wong, T.K.F.
Lam, T.W.
Sung, W.-K. 
Cheung, B.W.Y.
Yiu, S.M.
Keywords: dynamic programming
secondary structure
Issue Date: 2011
Citation: Wong, T.K.F., Lam, T.W., Sung, W.-K., Cheung, B.W.Y., Yiu, S.M. (2011). Structural alignment of RNA with complex pseudoknot structure. Journal of Computational Biology 18 (1) : 97-108. ScholarBank@NUS Repository.
Abstract: The secondary structure of an ncRNA molecule is known to play an important role in its biological functions. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, existing algorithms cannot handle complex pseudoknot structures which are found in nature. In this article, we propose algorithms to handle two types of complex pseudoknots: simple non-standard pseudoknots and recursive pseudoknots. Although our methods are not designed for general pseudoknots, it already covers all known ncRNAs in both Rfam and PseudoBase databases. An evaluation of our algorithms shows that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA. © Copyright 2011, Mary Ann Liebert, Inc.
Source Title: Journal of Computational Biology
ISSN: 10665277
DOI: 10.1089/cmb.2009.0275
Appears in Collections:Staff Publications

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