Structural Alignment of RNA with Complex Pseudoknot Structure

  • Thomas K. F. Wong
  • T. W. Lam
  • Wing-Kin Sung
  • S. M. Yiu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5724)


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 paper, 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 cover all known ncRNAs in both Rfam and PseudoBase databases. A preliminary evaluation on our algorithms show that it is useful to identify ncRNA molecules in other species which are in the same family of a known ncRNA.


Structural alignment non-coding RNA pseudoknots 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Thomas K. F. Wong
    • 1
  • T. W. Lam
    • 1
  • Wing-Kin Sung
    • 2
  • S. M. Yiu
    • 1
  1. 1.Department of Computer ScienceThe University of Hong KongHong Kong
  2. 2.School of ComputingNational University of SingaporeSingapore

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