Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Pattern discovery in RNA secondary structure using affix trees
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
The affix array data structure and its applications to RNA secondary structure analysis
Theoretical Computer Science
Tree template matching in ranked ordered trees by pushdown automata
CIAA'11 Proceedings of the 16th international conference on Implementation and application of automata
Computing all subtree repeats in ordered ranked trees
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Computing all subtree repeats in ordered trees
Information Processing Letters
Tree template matching in ranked ordered trees by pushdown automata
Journal of Discrete Algorithms
Tree template matching in unranked ordered trees
Journal of Discrete Algorithms
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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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.