A technique to find multiple motif occurrences in a biomolecular sequence

Abstract

A new flexible and efficient search technique has been recently introduced which includes two main components, a generalized profile syntax serving as motif definition language, and a motif search technique finding multiple instances of a motif in the same sequence. The generalized profile structure is presented in detail, as well as the alignment and score notions which constitute the foundations of modern motif descriptors. In order to mathematically model these notions, given a sequence and a profile, an alignment graph is built, so that a motif occurrence in the sequence is equivalent to a path in this directed graph. A mathematical statement of the motif search problem is formulated based on “reasonable” biological considerations. This statement together with an alignment disjointness definition allows finally to implement an efficient algorithm solving the stated problem exactly.