Fast detection of common sequence structure patterns in RNAs

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. (C) 2006 Elsevier B.V. All rights reserved.