Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
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)
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)
Bremges, A., Schirmer, S., Giegerich, R.: Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics 11, 222 (2010)
Giegerich, R., Voss, B., Rehmsmeier, M.: Abstract shapes of RNA. Nucleic Acids Research 32(16), 4843–4851 (2004)
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, http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.12
Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol. 162(3), 705–708 (1982)
Hoechsmann, M., Toeller, T., Giegerich, R., Kurtz, S.: Local similarity in RNA secondary structures. Proc. IEEE Comput. Soc. Bioinform. Conf. 2, 159–168 (2003)
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)
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)
Jiang, T., Wang, L., Zhang, K.: Alignment of trees – an alternative to tree edit. Theor. Comput. Sci., 143 (1): 137–148 (1995)
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)
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)
Reeder, J., Giegerich, R.: Consensus Shapes: An Alternative to the Sankoff Algorithm for RNA Consensus Structure Prediction. Bioinformatics 21(17), 3516–3523 (2005)
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)
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)
Schirmer, S.: Comparing forests. PhD thesis, Faculty of Technology, Bielefeld University (to appear)
Tai, K.C.: The tree-to-tree correction problem. J. ACM 26, 422–433 (1979)
Touzet, H.: Tree edit distance with gaps. Inf. Process. Lett. 85(3), 123–129 (2003)
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)
Zhang, K., Shasha, D.: Simple fast algorithms for the editing distance between trees and related problems. SIAM J. Comput. 18(6), 1245–1262 (1989)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Schirmer, S., Giegerich, R. (2011). Forest Alignment with Affine Gaps and Anchors. In: Giancarlo, R., Manzini, G. (eds) Combinatorial Pattern Matching. CPM 2011. Lecture Notes in Computer Science, vol 6661. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21458-5_11
Download citation
DOI: https://doi.org/10.1007/978-3-642-21458-5_11
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-21457-8
Online ISBN: 978-3-642-21458-5
eBook Packages: Computer ScienceComputer Science (R0)