Forest Alignment with Affine Gaps and Anchors

  • Stefanie Schirmer
  • Robert Giegerich
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6661)


We present two enhancements to Jiang’s tree alignment algorithm, motivated by experience with its use for RNA structure alignment. One enhancement is the introduction of an affine gap model, which can be accommodated with a runtime increase by a constant factor. The second enhancement is a speed-up of the alignment algorithm when certain nodes in the trees are pre-aligned by a so-called anchoring. Both enhancements are included in a new implementation of the tool RNAforester. We also argue that tree alignment should be parameterized by a user-described set of edit operations, generalizing over the traditional, atomic edit operations.


RNA structure alignment forest alignment affine gap costs anchored alignment 


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  1. 1.
    Backofen, R., Landau, G.M., Möhl, M., Tsur, D., Weimann, O.: Fast RNA Structure Alignment for Crossing Input Structures. In: Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching, pp. 236–248 (2009)Google Scholar
  2. 2.
    Blin, G., Touzet, H.: How to compare arc-annotated sequences: The alignment hierarchy. In: Crestani, F., Ferragina, P., Sanderson, M. (eds.) SPIRE 2006. LNCS, vol. 4209, pp. 291–303. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  3. 3.
    Bremges, A., Schirmer, S., Giegerich, R.: Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics 11, 222 (2010)CrossRefGoogle Scholar
  4. 4.
    Giegerich, R., Voss, B., Rehmsmeier, M.: Abstract shapes of RNA. Nucleic Acids Research 32(16), 4843–4851 (2004)CrossRefGoogle Scholar
  5. 5.
    Giegerich, R., Höner zu Siederdissen, C.: Semantics and Ambiguity of Stochastic RNA Family Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(2), 499–516 (2011), DOI, CrossRefGoogle Scholar
  6. 6.
    Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol. 162(3), 705–708 (1982)CrossRefGoogle Scholar
  7. 7.
    Hoechsmann, M., Toeller, T., Giegerich, R., Kurtz, S.: Local similarity in RNA secondary structures. Proc. IEEE Comput. Soc. Bioinform. Conf. 2, 159–168 (2003)Google Scholar
  8. 8.
    Hoechsmann, M., Voss, B., Giegerich, R.: Pure multiple RNA secondary structure alignments: A progressive profile approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1, 53–62 (2004)CrossRefGoogle Scholar
  9. 9.
    Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., Schuster, P.: Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie / Chemical Monthly 125(2), 167–188 (1994)CrossRefGoogle Scholar
  10. 10.
    Jiang, T., Wang, L., Zhang, K.: Alignment of trees – an alternative to tree edit. Theor. Comput. Sci., 143 (1): 137–148 (1995)MathSciNetCrossRefMATHGoogle Scholar
  11. 11.
    Lozano, A., Pinter, R.Y., Rokhlenko, O., Valiente, G., Ziv-Ukelson, M.: Seeded Tree Alignment. IEEE/ACM Trans. Comput. Biol. Bioinformatics 5(4), 503–513 (2008)CrossRefGoogle Scholar
  12. 12.
    Möhl, M., Will, S., Backofen, R.: Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. In: Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching, pp. 69–81 (2008)Google Scholar
  13. 13.
    Reeder, J., Giegerich, R.: Consensus Shapes: An Alternative to the Sankoff Algorithm for RNA Consensus Structure Prediction. Bioinformatics 21(17), 3516–3523 (2005)CrossRefGoogle Scholar
  14. 14.
    Ritchie, W., Legendre, M., Gautheret, D.: RNA stem loops: to be or not to be cleaved by RNAse III. RNA 13(4), 457–462 (2007)CrossRefGoogle Scholar
  15. 15.
    Rosselló, F., Valiente, G.: An algebraic view of the relation between largest common subtrees and smallest common supertrees. Theor. Comput. Sci. 362(1), 33–53 (2006)MathSciNetCrossRefMATHGoogle Scholar
  16. 16.
    Schirmer, S.: Comparing forests. PhD thesis, Faculty of Technology, Bielefeld University (to appear)Google Scholar
  17. 17.
    Tai, K.C.: The tree-to-tree correction problem. J. ACM 26, 422–433 (1979)MathSciNetCrossRefMATHGoogle Scholar
  18. 18.
    Touzet, H.: Tree edit distance with gaps. Inf. Process. Lett. 85(3), 123–129 (2003)MathSciNetCrossRefMATHGoogle Scholar
  19. 19.
    Touzet, H.: A linear tree edit distance algorithm for similar ordered trees. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 334–345. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  20. 20.
    Zhang, K., Shasha, D.: Simple fast algorithms for the editing distance between trees and related problems. SIAM J. Comput. 18(6), 1245–1262 (1989)MathSciNetCrossRefMATHGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Stefanie Schirmer
    • 1
  • Robert Giegerich
    • 1
  1. 1.Practical Computer ScienceBielefeld UniversityBielefeldGermany

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