The analysis of hybrid trie structures
Proceedings of the ninth annual ACM-SIAM symposium on Discrete algorithms
An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Breadth-first search strategies for trie-based syntactic pattern recognition
Pattern Analysis & Applications
Tries in data retrieval and syntactic pattern recognition
Tries in data retrieval and syntactic pattern recognition
The affix array data structure and its applications to RNA secondary structure analysis
Theoretical Computer Science
A grammatical approach to RNA-RNA interaction prediction
Pattern Recognition
Bioinformatics
RISOTTO: fast extraction of motifs with mismatches
LATIN'06 Proceedings of the 7th Latin American conference on Theoretical Informatics
Trie-based apriori motif discovery approach
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
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RNA interactions are fundamental to a multitude of cellular processes including post-transcriptional gene regulation. Although much progress has been made recently at developing fast algorithms for predicting RNA interactions, much less attention has been devoted to the development of efficient algorithms and data structures for locating RNA interaction patterns. We present two algorithms for locating all the occurrences of a given interaction pattern in a set of RNA sequences. The baseline algorithm implements an exhaustive backtracking search. The second algorithm also finds all the matches, but uses additional data structures in order to considerably decrease the execution time, sometimes by one order of magnitude. The worst case memory requirement for the later algorithm increases exponentially with the input pattern length and does not depend on the database size, making it practical for large databases. The performance of the algorithms is illustrated with an application for locating RNA elements in a Diplonemid genome.