A polynomial time equivalence between DNA sequencing and the exact perfect matching problem

We investigate the computational complexity of a combinatorial problem that arises in DNA sequencing by hybridization: The input consists of an integer together with a set S of words of length k over the four symbols A, C, G, T . The problem is to decide whether there exists a word of length that contains every word in S at least once as a subword, and does not contain any other subword of length k. The computational complexity of this problem has been open for some time, and it remains open. What we prove is that this problem is polynomial time equivalent to the exact perfect matching problem in bipartite graphs, which is another infamous combinatorial optimization problem of unknown computational complexity. c 2006 Elsevier B.V. All rights reserved.

• Type: Journal
• Year: 2007
• Where: DISOPT
• Authors: Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, Petra Schuurman, Gerhard J. Woeginger
• Keywords: Combinatorial Problem, Computational Complexity, DISOPT 2007, Perfect Matching Problem