Abstract
We developed a dynamic programming approach of computing common sequence/structure patterns between two RNAs given by their sequence and secondary structures. Common patterns between two RNAs are meant to share the same local sequential and structural properties. Nucleotides which are part of an RNA are linked together due to their phosphodiester or hydrogen bonds. These bonds describe the way how nucleotides are involved in patterns and thus delivers a bond-preserving matching definition. Based on this definition, 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, respectively. Our method is useful for describing and detecting local motifs and for detecting local regions of large RNAs although they do not share global similarities. An implementation is available in C++ and can be obtained by contacting one of the authors.
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Backofen, R., Siebert, S. (2004). Fast Detection of Common Sequence Structure Patterns in RNAs. In: Apostolico, A., Melucci, M. (eds) String Processing and Information Retrieval. SPIRE 2004. Lecture Notes in Computer Science, vol 3246. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30213-1_12
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DOI: https://doi.org/10.1007/978-3-540-30213-1_12
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