An Edit Distance Between RNA Stem-Loops

  • Valentin Guignon
  • Cedric Chauve
  • Sylvie Hamel
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3772)


We introduce the notion of conservative edit distance and mapping between two RNA stem-loops. We show that unlike the general edit distance between RNA secondary structures, the conservative edit distance can be computed in polynomial time and space, and we describe an algorithm for this problem. We show how this algorithm can be used in the more general problem of complete RNA secondary structures comparison.


Internal Node Dynamic Programming Algorithm Conservative Mapping Edit Operation Indexing Pair 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Valentin Guignon
    • 1
  • Cedric Chauve
    • 2
  • Sylvie Hamel
    • 3
  1. 1.Programme de BioinformatiqueUniversité de MontréalMontréalCanada
  2. 2.LaCIM, Département d’InformatiqueUniversité du Québec à MontréalMontréalCanada
  3. 3.LBIT, DIROUniversité de MontréalMontréalCanada

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