Hardness results on the gapped consecutive-ones property problem

Abstract

Motivated by problems in comparative genomics and paleogenomics, we study the computational complexity of the Gapped Consecutive-Ones Property ((k,δ)-C1P) Problem: given a binary matrix M and two integers k and δ, decide if the columns of M can be permuted such that each row contains at most k blocks of ones and no two neighboring blocks of ones are separated by a gap of more than δ zeros. The classical C1P decision problem, which is known to be polynomial-time solvable is equivalent to the (1,0)-C1P problem. We extend our earlier results on this problem [C. Chauve, J. Mauch, M. Patterson, On the gapped consecutive-ones property, in: Proceedings of the European Conference on Combinatorics, Graphs Theory and Applications (EuroComb), in: Electronic Notes in Discrete Mathematics, vol. 34, 2009, pp. 121–125] to show that for every k≥2,δ≥1,(k,δ)≠(2,1), the (k,δ)-C1P Problem is NP-complete, and that for every δ≥1, the (∞,δ)-C1P Problem is NP-complete. On the positive side, we also show that if k,δ and the maximum degree of M are constant, the problem is related to the classical Graph Bandwidth Problem and can be solved in polynomial time using a variant of an algorithm of Saxe [J.B. Saxe, Dynamic-programming algorithms for recognizing small-bandwidth graphs in polynomial time, SIAM Journal on Algebraic and Discrete Methods 1 (4) (1980) 363–369].