Identification of structured motifs

Structured motifs consist of two simpler patterns (half-sites) separated from each other by a gap, with no restriction on the nucleotides that may occur within the gap. This paper proposes a new algorithm to identify structured motifs. First, a simpler motif searching algorithm is used to search for half-sites. Candidate structured motif models are then evaluated, based on the relative frequency of occurrence of half-sites (not attributable to randomness), and the distribution of gap length. Unlike other recent structured motif detection algorithms, the new algorithm does not require the gap length to be prespecified.