Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Approximating the 2-interval pattern problem
ESA'05 Proceedings of the 13th annual European conference on Algorithms
Extracting constrained 2-interval subsets in 2-interval sets
Theoretical Computer Science
Common structured patterns in linear graphs: approximation and combinatorics
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
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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 $\{-structured patterns and disjoint interval ground set, is NP-hard.