Algorithms for pattern matching and discovery in RNA secondary structure

Text-indexing structures provide significant advantages in the solution of many problems related to string analysis and comparison, and are nowadays widely used in the analysis of biological sequences. In this paper, we present some applications of affix trees to problems of exact and approximate pattern matching and discovery in RNA sequences. By allowing bidirectional search for symmetric patterns in the sequences, affix trees permit to discover and locate in the sequences patterns describing not only sequence regions, but also containing information about the secondary structure that a given region could form, with improvements in terms of theoretical and practical efficiency over the existing methods. The search can be either exact or approximate, where the approximation can be defined simultaneously both for the sequence and the structure of patterns. The approach presented in this paper could provide significant help in the analysis of RNA sequences, where the functional motifs often involve not only sequence, but also the structural constraints.