An Efficient Algorithm for Planted Composit Motif Extraction

In this paper we present an algorithm for the problem of planted structured motif extraction from a set of sequences. This problem is strictly related to the structured motif extraction problem, which has many important applications in molecular biology. We propose an algorithm that uses a simple two-stage approach: first it extracts simple motifs, then the simple motifs are combined in order to extract structured motifs. We compare our algorithm with existing algorithms whose code is available, and which are based on more complex approaches. Our experiments show that, even if in general the problem is NP-hard, our algorithm is able to handle complex instances of the problem in a reasonable amount of time.