Rapid dynamic programming algorithms for RNA secondary structure
Advances in Applied Mathematics
Geometric applications of a matrix searching algorithm
SCG '86 Proceedings of the second annual symposium on Computational geometry
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
An almost linear time algorithm for generalized matrix searching
SIAM Journal on Discrete Mathematics
Sparse dynamic programming II: convex and concave 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
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
Algorithms for the Longest Common Subsequence Problem
Journal of the ACM (JACM)
A fast algorithm for computing longest common subsequences
Communications of the ACM
Data Structures and Algorithms
Data Structures and Algorithms
The Design and Analysis of Computer Algorithms
The Design and Analysis of Computer Algorithms
Sparse dynamic programming II: convex and concave cost functions
Journal of the ACM (JACM)
Chaining multiple-alignment fragments in sub-quadratic time
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
A new flexible algorithm for the longest common subsequence problem
Nordic Journal of Computing
Efficient Computation of All Longest Common Subsequences
SWAT '00 Proceedings of the 7th Scandinavian Workshop on Algorithm Theory
JOBIM '00 Selected papers from the First International Conference on Computational Biology, Biology, Informatics, and Mathematics
Algorithms for Transposition Invariant String Matching
STACS '03 Proceedings of the 20th Annual Symposium on Theoretical Aspects of Computer Science
Longest Common Subsequence from Fragments via Sparse Dynamic Programming
ESA '98 Proceedings of the 6th Annual European Symposium on Algorithms
Sparse LCS common substring alignment
Information Processing Letters
Finding anchors for genomic sequence comparison
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Information Processing Letters
Transposition invariant string matching
Journal of 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)
Fast algorithms for finding disjoint subsequences with extremal densities
Pattern Recognition
A graph approach to the threshold all-against-all substring matching problem
Journal of Experimental Algorithmics (JEA)
Fast Algorithms for Computing Tree LCS
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Fast algorithms for computing tree LCS
Theoretical Computer Science
Constraint-Based Strategy for Pairwise RNA Secondary Structure Prediction
EPIA '09 Proceedings of the 14th Portuguese Conference on Artificial Intelligence: Progress in Artificial Intelligence
Transposition invariant string matching
Journal of Algorithms
Multiple genome alignment: chaining algorithms revisited
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
A chaining algorithm for mapping cDNA sequences to multiple genomic sequences
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
Finding common structured patterns in linear graphs
Theoretical Computer Science
Solving longest common subsequence and related problems on graphical processing units
Software—Practice & Experience
EuroMPI'10 Proceedings of the 17th European MPI users' group meeting conference on Recent advances in the message passing interface
Approximation algorithms for speeding up dynamic programming and denoising aCGH data
Journal of Experimental Algorithmics (JEA)
Fast algorithms for finding disjoint subsequences with extremal densities
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
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 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
Efficient q-gram filters for finding all ε-matches over a given length
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Restricted transposition invariant approximate string matching under edit distance
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
A bibliography on computational molecular biology and genetics
Mathematical and Computer Modelling: An International Journal
Common structured patterns in linear graphs: approximation and combinatorics
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Homomorphic hashing for sparse coefficient extraction
IPEC'12 Proceedings of the 7th international conference on Parameterized and Exact Computation
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Dynamic programming solutions to a number of different recurrence equations for sequence comparison and for RNA secondary structure prediction 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 for these problems are given, when the weight functions used in the recurrences are taken to be linear. The time complexity of the 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.