Data structures and network algorithms
Data structures and network algorithms
Rapid dynamic programming algorithms for RNA secondary structure
Advances in Applied Mathematics
The least weight subsequence problem
SIAM Journal on Computing
The concave least-weight subsequence problem revisited
Journal of Algorithms
Speeding up dynamic programming with application to molecular biology
Theoretical Computer Science
Sequence comparison with mixed convex and concave costs
Journal of Algorithms
An almost linear time algorithm for generalized matrix searching
SIAM Journal on Discrete Mathematics
Applications of generalized matrix searching to geometric algorithms
Discrete Applied Mathematics - Computational combinatiorics
Sparse dynamic programming I: linear cost functions
Journal of the ACM (JACM)
The art of computer programming, volume 3: (2nd ed.) sorting and searching
The art of computer programming, volume 3: (2nd ed.) sorting and searching
The Design and Analysis of Computer Algorithms
The Design and Analysis of Computer Algorithms
Efficient dynamic programming using quadrangle inequalities
STOC '80 Proceedings of the twelfth annual ACM symposium on Theory of computing
Sparse dynamic programming I: linear cost functions
Journal of the ACM (JACM)
A sub-quadratic sequence alignment algorithm for unrestricted cost matrices
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
ISAAC '98 Proceedings of the 9th International Symposium on Algorithms and Computation
Longest Common Subsequence from Fragments via Sparse Dynamic Programming
ESA '98 Proceedings of the 6th Annual European Symposium on Algorithms
Challenges in the compilation of a domain specific language for dynamic programming
Proceedings of the 2006 ACM symposium on Applied computing
Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Two algorithms for LCS Consecutive Suffix Alignment
Journal of Computer and System Sciences
A graph approach to the threshold all-against-all substring matching problem
Journal of Experimental Algorithmics (JEA)
Review of automatic document formatting
Proceedings of the 9th ACM symposium on Document engineering
Constraint-Based Strategy for Pairwise RNA Secondary Structure Prediction
EPIA '09 Proceedings of the 14th Portuguese Conference on Artificial Intelligence: Progress in Artificial Intelligence
Sparse LCS common substring alignment
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
An improved algorithm for the longest common subsequence problem
Computers and Operations Research
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
Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A hyper-heuristic for the Longest Common Subsequence problem
Computational Biology and Chemistry
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
High-quality pagination for publishing
Software—Practice & Experience
A bibliography on computational molecular biology and genetics
Mathematical and Computer Modelling: An International Journal
Homomorphic hashing for sparse coefficient extraction
IPEC'12 Proceedings of the 7th international conference on Parameterized and Exact Computation
No need to justify your choice: pre-compiling line breaks to improve eBook readability
Proceedings of the 2013 ACM symposium on Document engineering
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Dynamic programming solutions to two recurrence equations, used to compute a sequence alignment from a set of matching fragments between two strings, and to predict RNA secondary structure, are considered. These recurrences are defined over a number of points that is quadratic in the input size; however, only a sparse set matters for the result. Efficient algorithms are given for solving these problems, when the cost of a gap in the alignment or a loop in the secondary structure is taken as a convex or concave function of the gap or loop length. The time complexity of our algorithms depends almost linearly on the number of points that need to be considered; when the problems are sparse, this results in a substantial speed-up over known algorithms.