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.
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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
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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
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