Rapid dynamic programming algorithms for RNA secondary structure
Advances in Applied Mathematics
Alignment of RNA base pairing probability matrices
Bioinformatics
Bioinformatics
Fast RNA Structure Alignment for Crossing Input Structures
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Sparse RNA Folding: Time and Space Efficient Algorithms
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
A worst-case and practical speedup for the RNA co-folding problem using the four-Russians idea
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Sparsification of RNA structure prediction including pseudoknots
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Fast RNA structure alignment for crossing input structures
Journal of Discrete Algorithms
Rich parameterization improves RNA structure prediction
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
Time and space efficient RNA-RNA interaction prediction via sparse folding
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Exact pattern matching for RNA structure ensembles
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Hi-index | 0.00 |
The current pairwise RNA (secondary) structural alignment algorithms are based on Sankoff's dynamic programming algorithm from 1985. Sankoff's algorithm requires O(N6) time and O(N4) space, where Ndenotes the length of the compared sequences, and thus its applicability is very limited. The current literature offers many heuristics for speeding up Sankoff's alignment process, some making restrictive assumptions on the length or the shape of the RNA substructures. We show how to speed up Sankoff's algorithm in practice via non-heuristic methods, without compromising optimality. Our analysis shows that the expected time complexity of the new algorithm is O(N4驴(N)), where 驴(N) converges to O(N), assuming a standard polymer folding model which was supported by experimental analysis. Hence our algorithm speeds up Sankoff's algorithm by a linear factor on average. In simulations, our algorithm speeds up computation by a factor of 3-12 for sequences of length 25-250.Availability:Code and data sets are available, upon request.