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)
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Lifting Prediction to Alignment of RNA Pseudoknots
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Fast RNA Structure Alignment for Crossing Input Structures
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Comparing RNA structures: towards an intermediate model between the edit and the LAPCS problems
BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
Fast RNA structure alignment for crossing input structures
Journal of Discrete Algorithms
Hi-index | 0.00 |
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.