Abstract
Contact maps are concepts that are often used to represent structural information in molecular biology. The contact map pattern matching (CMPM) problem is to decide if a contact map (called the pattern) is a substructure of another contact map (called the target). In general, the problem is NP-hard, but when there are restrictions on the form of the pattern, the problem can, in some case, be solved in polynomial time. In particular, a polynomial time algorithm has been proposed [1] for the case when the patterns are so-called crossing contact maps. In this paper we show that the problem is actually NP-hard, and show a flaw in the proposed polynomial-time algorithm. Through the same method, we also show that a related problem, namely, the 2-interval patten matching problem with \(\{<, \between\}\) -structured patterns and disjoint interval ground set, is NP-hard.
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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
Gramm, J.: A polynomial-time algorithm for the matching of crossing contact-map patterns. IEEE/ACM Trans. Comput. Biol. Bioinformatics 1, 171–180 (2004)
Goldman, D., Papadimitriou, C., Istrail, S.: Algorithmic aspects of protein structure similarity. In: Proc. 40th Symp. on Foundations of Computer Science FOCS 1999, p. 512. IEEE Computer Society, Los Alamitos (1999)
Vialette, S.: On the computational complexity of 2-interval pattern matching problems. Theor. Comput. Sci. 312, 223–249 (2004)
Blin, G., Fertin, G., Vialette, S.: New results for the 2-interval problem. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 311–322. Springer, Heidelberg (2004)
Crochemore, M., Hermelin, D., Landau, G., Vialette, S.: Approximating the 2-interval pattern problem. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol. 3669, pp. 426–437. Springer, Heidelberg (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Li, S.C., Li, M. (2006). On the Complexity of the Crossing Contact Map Pattern Matching Problem. In: Bücher, P., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science(), vol 4175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11851561_22
Download citation
DOI: https://doi.org/10.1007/11851561_22
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-39583-6
Online ISBN: 978-3-540-39584-3
eBook Packages: Computer ScienceComputer Science (R0)