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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)

Abstract

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.

Keywords

Internal Node Dynamic Programming Algorithm Conservative Mapping Edit Operation Indexing Pair 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Allali, J., Sagot, M.-F.: A new distance for high level RNA secondary structure comparison. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2(1), 4–14 (2005)CrossRefGoogle Scholar
  2. 2.
    Backofen, R., Will, S.: Local sequence-structure motifs in RNA. J. Bioinform. Comput. Biol. 2(4), 681–698 (2004)CrossRefGoogle Scholar
  3. 3.
    Blin, G., Fertin, G., Sinoquet, C.: RNA sequences and the EDIT(NESTED, NESTED) problem. Report RR-IRIN-03.07, IRIN, Nantes, France (2003)Google Scholar
  4. 4.
    Couzin, J.: Breakthrough of the year: small RNAs make big splash. Science 298, 2296–2297 (2002)CrossRefGoogle Scholar
  5. 5.
    Gusfield, D.: Algorithms on strings, trees and sequences. Cambridge University Press, Cambridge (1997)zbMATHCrossRefGoogle Scholar
  6. 6.
    Höchsmann, M., Töller, T., Giegerich, R., Kurtz, S.: Local similarity in RNA secondary structures. In: 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), pp. 159–169. IEEE Computer Society, Los Alamitos (2003)Google Scholar
  7. 7.
    Hofacker, I.L.: Vienna RNA secondary structure server. Nucleic Acids Res. 31(13), 3429–3431 (2003)CrossRefGoogle Scholar
  8. 8.
    Jiang, T., Lin, G., Ma, B., Zhang, K.: A general edit distance between RNA structures. J. Comput. Biol. 9(2), 371–388 (2002)CrossRefGoogle Scholar
  9. 9.
    Shapiro, B.A., Zhang, K.: Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci. 6(4), 309–318 (1988)Google Scholar
  10. 10.
    Zhang, K., Shasha, D.: Simple fast algorithms for the editing distance between trees and related problems. SIAM J. Comput. 18(6), 1245–1262 (1989)zbMATHCrossRefMathSciNetGoogle Scholar

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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