Comparing, Ranking, and Filtering Motifs with Character Classes: Application to Biological Sequences Analysis

This chapter provides a characterization of motifs with character classes, following with the notion of motif priority for comparing and ranking different motifs together. The authors introduce the concept of underlying motifs for filtering any set of motifs with character classes into a new set that is linear in size with respect to a reference sequence. They present an algorithm to compute this new set exploiting the notions. Finally, they discuss some preliminary results on the identification of signals in protein sequences by means of underlying motifs. They have proved several theoretical results that support the validity of these fundamental properties. Most important, their motif priority rule along with the notion of underlying motifs has proved to be valuable for the analysis of biological sequences.