Novel Tree Edit Operations for RNA Secondary Structure Comparison

  • Julien Allali
  • Marie-France Sagot
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)


We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two novel operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion and relabelling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.


tree comparison edit operation distance RNA secondary structure 


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  1. 1.
    Bouthinon, D., Soldano, H.: A new method to predict the consensus secondary structure of a set of unaligned RNA sequences. Bioinformatics 15(10), 785–798 (1999)CrossRefGoogle Scholar
  2. 2.
    Brown, J.W.: The ribonuclease p database. Nucleic Acids Research 24(1), 314 (1999)CrossRefGoogle Scholar
  3. 3.
    el Mabrouk, N., Lisacek, F.: Very fast identification of RNA motifs in genomic DNA. application to tRNA search in the yeast genome. J. Mol. Biol. 264(1), 46–55 (1996)CrossRefGoogle Scholar
  4. 4.
    Winkelmans, T., Wuyts, J., Van de Peer, Y., De Wachter, R.: The european database on small subunit ribosomal rna. Nucleic Acids Research 30(1), 183–185 (2002)CrossRefGoogle Scholar
  5. 5.
    Lisacek, F., Diaz, Y., Michel, F.: Automatic identification of group I intron cores in genomic DNA sequences. J. Mol. Biol. 235(4), 1206–1217 (1994)CrossRefGoogle Scholar
  6. 6.
    Shapiro, B.A., Zhang, K.: Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci. 6(4), 309–318 (1990)Google Scholar
  7. 7.
    Shapiro, B.: An algorithm for multiple rna secondary structures. Comput. Appl. Biosci. 4(3), 387–393 (1988)Google Scholar
  8. 8.
    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
  9. 9.
    Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31(13), 3406–3415 (2003)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Julien Allali
    • 1
  • Marie-France Sagot
    • 2
    • 3
  1. 1.Institut Gaspard-MongeUniversité de Marne-la-Vallée, Cité DescartesMarne-la-Vallée Cedex 2France
  2. 2.Inria Rhône-Alpes, Université Claude Bernard, Lyon IVilleurbanne cedexFrance
  3. 3.King’s CollegeLondonUK

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