Rapid dynamic programming algorithms for RNA secondary structure

Authors:
Michael S Waterman;Temple F Smith
Affiliations:
Departments of Mathematics and of Biological Sciences, University of Southern California, Los Angeles, California 90089-1113 U.S.A.;Department of Biostatistics, Harvard University, 44 Binney Street, Boston, Massachusetts 02115 U.S.A.
Venue:
Advances in Applied Mathematics
Year:
1986

Citing 0
Cited 18

Sparse dynamic programming I: linear cost functions

Journal of the ACM (JACM)
Sparse dynamic programming II: convex and concave cost functions

Journal of the ACM (JACM)
Internal loops in RNA secondary structure prediction

RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
On-line dynamic programming with applications to the prediction of RNA secondary structure

SODA '90 Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms
Sparse dynamic programming

SODA '90 Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms
Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages

ISAAC '98 Proceedings of the 9th International Symposium on Algorithms and Computation
A Faster Algorithm for RNA Co-folding

WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
RNA pseudoknot structures with arc-length ≥3 and stack-length ≥σ

Discrete Applied Mathematics
A matrix algorithm for RNA secondary structure prediction

PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
An experimental study of optimizing bioinformatics applications

IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Approximation algorithms for speeding up dynamic programming and denoising aCGH data

Journal of Experimental Algorithmics (JEA)
Approximate dynamic programming using halfspace queries and multiscale Monge decomposition

Proceedings of the twenty-second annual ACM-SIAM symposium on Discrete Algorithms
Monge properties of sequence alignment

Theoretical Computer Science
A high-throughput approach for associating microRNAs with their activity conditions

RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
An efficient dynamic programming algorithm and implementation for RNA secondary structure prediction

ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
A study of accessible motifs and RNA folding complexity

RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
A bibliography on computational molecular biology and genetics

Mathematical and Computer Modelling: An International Journal
RNA Secondary Structure Prediction Using Soft Computing

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Quantified Score

Hi-index	0.00

Visualization

Abstract

Prediction of RNA secondary structure from the linear RNA sequence is an important mathematical problem in molecular biology. Dynamic programming methods are currently the most useful computer technique but are frequently very expensive in running time. In this paper new dynamic programming algorithms are presented which reduce the required computation. The first polynomial time algorithm is given for predicting general secondary structure.