Incremental inference of relational motifs with a degenerate alphabet

Abstract

In this paper we define a new class of problems that generalizes that of finding repeated motifs. The novelty lies in the addition of constraints on the motifs in terms of relations that must hold between pairs of elements of the motifs. For this class of problems we give an algorithm that is a suitable extension of the KMR [3] paradigm and, in particular, of the KMRC [7] as it uses a degenerate alphabet. The algorithm contains several improvements with respect to [7] that result especially useful when - as it is required for relational motifs - the inference is made by partially overlapping shorter motifs. The efficiency, correctness and completeness of the algorithm is assured by several nontrivial properties. Finally, we list some possible applications and we focus on one of them: the study of 3D structures of proteins. © Springer-Verlag Berlin Heidelberg 2005.