Abstract
We address the problem of approximating the 2-Interval Pattern problem over its various models and restrictions. This problem, which is motivated by RNA secondary structure prediction, asks to find a maximum cardinality subset of a 2-interval set with respect to some prespecified model. For each such model, we give varying approximation quality depending on the different possible restrictions imposed on the input 2-interval set.
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References
Akutsu, T.: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Applied Mathematics 104, 45–62 (2000)
Bar-Yehuda, R., Halldorsson, M.M., Naor, J., Shachnai, H., Shapira, I.: Scheduling spit intervals. In: Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2002), pp. 732–741 (2002)
Blin, G., Fertin, G., Vialette, S.: New results for the 2-interval pattern problem. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 311–322. Springer, Heidelberg (2004)
Dagan, I., Golumbic, M.C., Pinter, R.Y.: Trapezoid graphs and their coloring. Discrete Applied Mathematics 21, 35–46 (1988)
Felsner, S., Müller, R., Wernisch, L.: Trapezoid graphs and generalizations: Geometry and algorithms. Discrete Applied Mathematics 74, 13–32 (1997)
Gavril, F.: Algorithms for minimum coloring, maximum clique, minimum covering by cliques and maximum independent set of a chordal graph. SIAM Journal on Computing 1, 180–187 (1972)
Golumbic, M.C.: Algorithmic graph theory and perfect graphs. Academic Press, New York (1980)
Ieong, S., Kao, M.Y., Lam, T.W., Sung, W.K., Yiu, S.M.: Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs. In: Proceedings of the 2nd Symposium on Bioinformatics and Bioengineering (BIBE 2002), pp. 183–190 (2002)
Lyngsø, R.B., Pedersen, C.N.S.: RNA pseudoknot prediction in energy based models. Journal of Computational Biology 7, 409–428 (2000)
McKee, T.A., McMorris, F.R.: Topics in intersection graph theory. SIAM monographs on discrete mathematics and applications (1999)
Vialette, S.: On the computational complexity of 2-interval pattern matching problems. Theoretical Computer Science 312, 335–379 (2004)
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Crochemore, M., Hermelin, D., Landau, G.M., Vialette, S. (2005). Approximating the 2-Interval Pattern Problem. In: Brodal, G.S., Leonardi, S. (eds) Algorithms – ESA 2005. ESA 2005. Lecture Notes in Computer Science, vol 3669. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11561071_39
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DOI: https://doi.org/10.1007/11561071_39
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29118-3
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