Computing Similarity between RNA Structures
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Finding Common Subsequences with Arcs and Pseudoknots
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Computing Similarity Between RNA Secondary Structures
INTSYS '98 Proceedings of the IEEE International Joint Symposia on Intelligence and Systems
Computing similarity between RNA strings
Computing similarity between RNA strings
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A New Distance for High Level RNA Secondary Structure Comparison
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An optimal decomposition algorithm for tree edit distance
ICALP'07 Proceedings of the 34th international conference on Automata, Languages and Programming
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This paper presents the first polynomial time algorithm for finding common RNA substructures that include pseudoknots and similar structures. While a more general problem is known to be NP-hard, this algorithm exploits special features of RNA structures to match RNA bonds correctly in polynomial time. Although the theoretical upper bound on the algorithm@?s time and space usage is high, the data-driven nature of its computation enables it to avoid computing unnecessary cases, dramatically reducing the actual running time. The algorithm works well in practice, and has been tested on sample RNA structures that include pseudoknots and pseudoknot-like tertiary structures.