A Constraint Programming Approach for Enumerating Motifs in a Sequence

In this paper we propose a constraint programming approach for enumerating all frequent patterns with wildcards in a given sequence. To reduce the search space, we show that the anti-monotonicity property of frequent patterns can be dynamically encoded using no good recording based approach. Finally, the constraints network is encoded as a Boolean formula. This last step allows us to exploit the efficiency of modern SAT solvers and particularly their clauses learning component. Preliminary experiments on real world data show the feasibility of our approach in practice.