A sub-quadratic sequence alignment algorithm for unrestricted cost matrices
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Parallel dynamic programming for solving the string editing problem on a CGM/BSP
Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Approximate Periods of Strings
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Discovering instances of poetic allusion from anthologies of classical Japanese poems
Theoretical Computer Science
Implementing approximate regularities extended abstract
ICCMSE '03 Proceedings of the international conference on Computational methods in sciences and engineering
Occurrence and substring heuristics for δ-matching
Fundamenta Informaticae - Special issue on computing patterns in strings
Sparse LCS common substring alignment
Information Processing Letters
Multiple-source shortest paths in planar graphs
SODA '05 Proceedings of the sixteenth annual ACM-SIAM symposium on Discrete algorithms
FireμSat: meeting the challenge of detecting microsatellites in DNA
SAICSIT '06 Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing countries
Longest common subsequence problem for unoriented and cyclic strings
Theoretical Computer Science
Linear time algorithm for the longest common repeat problem
Journal of Discrete Algorithms
Discrete Applied Mathematics - 12th annual symposium on combinatorial pattern matching (CPM)
Two algorithms for LCS Consecutive Suffix Alignment
Journal of Computer and System Sciences
Multiple source shortest paths in a genus g graph
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Efficient algorithms for finding interleaving relationship between sequences
Information Processing Letters
An all-substrings common subsequence algorithm
Discrete Applied Mathematics
Approximate labelled subtree homeomorphism
Journal of Discrete Algorithms
Sequence Alignment Algorithms for Run-Length-Encoded Strings
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Semi-local longest common subsequences in subquadratic time
Journal of Discrete Algorithms
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Dynamic Edit Distance Table under a General Weighted Cost Function
SOFSEM '10 Proceedings of the 36th Conference on Current Trends in Theory and Practice of Computer Science
Discrete Applied Mathematics
Sparse LCS common substring alignment
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
STACS'07 Proceedings of the 24th annual conference on Theoretical aspects of computer science
Two element unavoidable sets of partial words
DLT'07 Proceedings of the 11th international conference on Developments in language theory
Combinatorics on partial word correlations
Journal of Combinatorial Theory Series A
New algorithms for efficient parallel string comparison
Proceedings of the twenty-second annual ACM symposium on Parallelism in algorithms and architectures
A fully compressed algorithm for computing the edit distance of run-length encoded strings
ESA'10 Proceedings of the 18th annual European conference on Algorithms: Part I
Multiplication algorithms for Monge matrices
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
New complexity results for the k-covers problem
Information Sciences: an International Journal
Alignment with non-overlapping inversions in O(n3)-time
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
All semi-local longest common subsequences in subquadratic time
CSR'06 Proceedings of the First international computer science conference on Theory and Applications
Exact distance oracles for planar graphs
Proceedings of the twenty-third annual ACM-SIAM symposium on Discrete Algorithms
On the complexity of sparse exon assembly
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Monge properties of sequence alignment
Theoretical Computer Science
Linear time algorithm for the generalised longest common repeat problem
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
Periodicity algorithms and a conjecture on overlaps in partial words
Theoretical Computer Science
Implementing approximate regularities
Mathematical and Computer Modelling: An International Journal
Occurrence and Substring Heuristics for δ-Matching
Fundamenta Informaticae - Computing Patterns in Strings
Alignments with non-overlapping moves, inversions and tandem duplications in O(n4) time
COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
RNA tree comparisons via unrooted unordered alignments
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Shortest-path queries in static networks
ACM Computing Surveys (CSUR)
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Weighted paths in directed grid graphs of dimension (m X n) can be used to model the string edit problem, which consists of obtaining optimal (weighted) alignments between substrings of A, |A|=m, and substrings of B, |B|=n. We build a data structure (in O(mn log m) time) that supports O(log m) time queries about the weight of any of the O(m2n) best paths from the vertices in column 0 of the graph to all other vertices. Using these techniques we present a simple O(n2 log n) time and $\Theta(n^2)$ space algorithm to find all (the locally optimal) approximate tandem (or nontandem) repeats xy within a string of size n. This improves (by a factor of log n) upon several previous algorithms for this problem and is the first algorithm to find all locally optimal repeats. For edit graphs with weights in {0, -1, 1}, a slight modification of our techniques yields an O(n2) algorithm for the cyclic string comparison problem, as compared to O(n2 log n) for the case of general weights.