An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots

  • Shinnosuke Seki
  • Satoshi Kobayashi
Conference paper
Part of the Proceedings in Information and Communications Technology book series (PICT, volume 1)


Pseudoknots, one of the key components of RNA secondary structures, have been almost systematically intractable because of the difficulty in modeling them. Tree adjoining grammars have proved to be promising for this problem but the question of how to make TAG-based applications practical enough to analyze RNAs of thousands nucleotides remains open. This paper addresses this problem. It makes use of biological properties of pseudoknots, the scarcity and short-bp property. Experiments showed that our algorithm can align RNAs of the length up to about 2400 nucleotides with biologically meaningful outputs extremely fast on the standard workstation environment. An executable version of our implementation is available at


Edit Distance Alignment Algorithm Pairwise Alignment Pseudoknotted Structure Tree Adjoining Grammar 


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Copyright information

© Springer Tokyo 2009

Authors and Affiliations

  • Shinnosuke Seki
    • 1
  • Satoshi Kobayashi
    • 2
  1. 1.Department of Computer ScienceUniversity of Western OntarioLondonCanada
  2. 2.Department of Computer ScienceThe University of Electro-CommunicationsTokyoJapan

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