On the computational complexity of 2-inteirval pattern matching problems

The focus of this paper is on the computational complexity of pattern matching problems over set of 2-intervals. These problems occur in the context of molecular biology when a structured pattern, i.e., a RNA secondary structure given in the form of a 2-interval pattern, has to be found in a sequence database. We show that finding a 2-interval pattern in a set of 2-intervals is a NP-complete problem even if no 2-interval of the pattern precedes the other, but can be solved in polynomial time for several interesting special cases. In particular, it is shown that the pseudo-knot free RNA secondary structure case is polynomial time solvable in our 2-interval formalism. Also, we investigate the computational complexity of finding the longest 2-interval pattern in a set of 2-intervals and prove several NP-completeness results as well as polynomial time solvable special cases. (C) 2003 Elsevier B.V. All rights reserved.