Abstract
The optimization of weighted string alignments is a well studied problem recurring in a number of application domains and can be solved efficiently. The problem becomes MAX-SNP-hard as soon as arbitrary pairwise dependencies among the alignment edges are introduced. We present a global propagator for this problem which is based on efficiently solving a relaxation of it. In the context of bioinformatics, the problem is known as alignment of arc-annotated sequences, which is e.g. used for comparing RNA molecules. For a restricted version of this alignment problem, we show that a constraint program based on our propagator is on par with state of the art methods. For the general problem with unrestricted dependencies, our tool constitutes the first available method with promising applications in this field.
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
Bauer, M., Klau, G.W., Reinert, K.: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics 8, 271 (2007)
Blin, G., Fertin, G., Rusu, I., Sinoquet, C.: Extending the hardness of RNA secondary structure comparison. In: Chen, B., Paterson, M., Zhang, G. (eds.) ESCAPE 2007. LNCS, vol. 4614, pp. 140–151. Springer, Heidelberg (2007)
Caprara, A., Lancia, G.: Structural alignment of large-size proteins via lagrangian relaxation. In: Proceedings of the Sixth Annual International Conference on Computational Biology (RECOMB 2002), pp. 100–108. ACM Press, New York (2002)
Gotoh, O.: An improved algorithm for matching biological sequences. Journal of Molecular Biology 162, 705–708 (1982)
Hoeve, W.-J., Pesant, G., Rousseau, L.-M.: On global warming: Flow-based soft global constraints. Journal of Heuristics 12(4-5), 347–373 (2006)
Jiang, T., Lin, G., Ma, B., Zhang, K.: A general edit distance between RNA structures. Journal of Computational Biology 9(2), 371–388 (2002)
Marinescu, R., Dechter, R.: And/or branch-and-bound search for combinatorial optimization in graphical models. Artif. Intell. 173(16-17), 1457–1491 (2009)
McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29(6-7), 1105–1119 (1990)
Möhl, M., Will, S., Backofen, R.: Lifting prediction to alignment of RNA pseudoknots. Journal of Computational Biology (2010) (accepted)
Smith, T.F., Waterman, M.S.: Comparison of biosequences. Adv. Appl. Math. 2, 482–489 (1981)
Trick, M.A.: A dynamic programming approach for consistency and propagation for knapsack constraints. Annals OR 118(1-4), 73–84 (2003)
Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., Backofen, R.: Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology 3(4), e65 (2007)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Dal Palù, A., Möhl, M., Will, S. (2010). A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies. In: Cohen, D. (eds) Principles and Practice of Constraint Programming – CP 2010. CP 2010. Lecture Notes in Computer Science, vol 6308. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15396-9_16
Download citation
DOI: https://doi.org/10.1007/978-3-642-15396-9_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-15395-2
Online ISBN: 978-3-642-15396-9
eBook Packages: Computer ScienceComputer Science (R0)