Abstract
We present a general setting for structure-sequence comparison in a large class of RNA structures, that unifies and generalizes a number of recent works on specific families of structures. Our approach is based on a tree decomposition of structures, and gives rise to a general parameterized algorithm having complexity in \(\mathcal{O}(N\cdot m^t)\), where N (resp. m) is the structure (resp. sequence) length, and the exponent t depends on the family of structures. For each family considered by previous approaches, our contribution specializes into an algorithm whose complexity either matches or outperforms previous solutions.
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
Arnborg, S., Corneil, D., Proskurowski, A.: Complexity of finding embeddings in a k-tree. SIAM J. Alg. Disc. Meth. 8(2), 277–284 (1987)
Blin, G., Denise, A., Dulucq, S., Herrbach, C., Touzet, H.: Alignment of RNA structures. IEEE/ACM Transactions on Computational Biology and Bioinformatics 7(2), 309–322 (2010)
Bodlaender, H.L.: Treewidth: Algorithmic Techniques and Results. In: Privara, I., Ružička, P. (eds.) MFCS 1997. LNCS, vol. 1295, pp. 19–36. Springer, Heidelberg (1997)
Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol. 162(3), 705–708 (1982)
Han, B., Dost, B., Bafna, V., Zhang, S.: Structural alignment of pseudoknotted RNA. Journal of Computational Biology 15(5), 489–504 (2008)
Jiang, T., Lin, G.H., Ma, B., Zhang, K.: A general edit distance between RNA structures. Journal of Computational Biology 9(2), 371–388 (2002)
Kahn, A.B.: Topological sorting of large networks. Communications of the ACM 5(11), 558–562 (1962)
Leontis, N.B., Westhof, E.: Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001)
Leontis, N.B., Westhof, E.: Analysis of RNA motifs. Curr. Opin. Struct. Biol. (13), 300–308 (2003)
Rødland, E.A.A.: Pseudoknots in RNA secondary structures: representation, enumeration, and prevalence. Journal of Computational Biology 13(6), 1197–1213 (2006)
Wong, T.K., Yiu, S.M.: Structural alignment of RNA with triple helix structure. Journal of Computational Biology 19(4), 365–378 (2012)
Wong, T., Lam, T., Sung, W., Cheung, B., Yiu, S.: Structural alignment of RNA with complex pseudoknot structure. Journal of Computational Biology 18(1) (2011)
Zhang, K., Wang, L., Ma, B.: Computing Similarity between RNA Structures. In: Crochemore, M., Paterson, M. (eds.) CPM 1999. LNCS, vol. 1645, pp. 281–293. Springer, Heidelberg (1999)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Rinaudo, P., Ponty, Y., Barth, D., Denise, A. (2012). Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots. In: Raphael, B., Tang, J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science(), vol 7534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33122-0_12
Download citation
DOI: https://doi.org/10.1007/978-3-642-33122-0_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-33121-3
Online ISBN: 978-3-642-33122-0
eBook Packages: Computer ScienceComputer Science (R0)