Implementing approximate regularities

Authors:
M. Christodoulakis;C. S. Iliopoulos;Kunsoo Park;Jeong Seop Sim
Affiliations:
-;-;-;-
Venue:
Mathematical and Computer Modelling: An International Journal
Year:
2005

Citing 4
Cited 1

All Highest Scoring Paths in Weighted Grid Graphs and Their Application to Finding All Approximate Repeats in Strings

SIAM Journal on Computing
Approximate periods of strings

Theoretical Computer Science
A Dynamic Edit Distance Table

COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
An Algorithm for Approximate Tandem Repeats

CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching

Nonlinear network optimization: an embedding vector space approach

IEEE Transactions on Evolutionary Computation

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Abstract

In this paper, we study approximate regularities of strings, that is, approximate periods, approximate covers, and approximate seeds. We explore their similarities and differences and we implement algorithms for solving the smallest distance approximate period/cover/seed problem and the restricted smallest approximate period/cover/seed/ problem in polynomial time, under a variety of distance rules (the Hamming distance, the edit distance, and the weighted edit distance). Then, we analyse our experimental results to find out the time complexity of the algorithms in practice.