An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees
IEEE Transactions on Pattern Analysis and Machine Intelligence
An Algorithm for Subgraph Isomorphism
Journal of the ACM (JACM)
Pseudoknots in RNA secondary structures
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Pattern Matching for Arc-Annotated Sequences
FST TCS '02 Proceedings of the 22nd Conference Kanpur on Foundations of Software Technology and Theoretical Computer Science
Local Similarity in RNA Secondary Structures
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
FastR: Fast Database Search Tool for Non-Coding RNA
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Alignment of RNA base pairing probability matrices
Bioinformatics
A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes
Theoretical Computer Science
Exact pattern matching for RNA structure ensembles
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
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We developed a dynamic programming approach for computing common exact sequential and structural patterns between two RNAs, given their sequences and their secondary structures. An RNA consists of a sequence of nucleotides and a secondary structure defined via bonds linking together complementary nucleotides. It is known that secondary structures are more preserved than sequences in the evolution of RNAs. We are able to compute all patterns between two RNAs in time O(nm) and space O(nm), where n and m are the lengths of the RNAs. Our method is useful for describing and detecting local motifs. It is especially suitable for finding similar regions of large RNAs that do not share global similarities. An implementation is available in C++ and can be obtained by contacting one of the authors.