Sampath K. Kannan, Eugene W. Myers  Home/Search
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Abstract: . In this paper we present an O(N 2 log 2 N) algorithm for finding the two non-overlapping substrings of a given string of length N which have the highest-scoring alignment between them. This significantly improves the previously best known bound of O(N 3 ) for the worst-case complexity of this problem. One of the central ideas in the design of this algorithm is that of partitioning a matrix into pieces in such a way that all submatrices of interest for this problem can be put together as ... (Update)
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...non heuristical developed so far for identifying tandem arrays. Other exact approaches either treated the case of tandem repeats only [22, 19], did not allow for errors [3, 5, 26, 46] or required generating all possible (not just valid) models of a given length [8, 10, 32]...
.... using the weighted edit distance as the similarity measure, can be found in [KM96, B95, S98, M92] and [BW94] Kannan and Meyers [KM93, KM96] describe a recursive algorithm for finding all highest scoring non overlapping alignments in O(n 2 log 2 n) time and O(n 2 log n)...
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BibTeX entry: (Update)
S. Kannan and E. Myers, "An algorithm for locating non-overlapping regions of maximum alignment score," Proc. 4th Symp. Combinatorial Pattern Matching, Springer-Verlag Lecture Notes in Computer Science, Vol. 648 (1993), 74--86. http://citeseer.ist.psu.edu/kannan93algorithm.html More
@inproceedings{ kannan93algorithm,
author = "S. K. Kannan and E. W. Myers",
title = "An algorithm for locating non-overlapping regions of maximum alignment score",
booktitle = "Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching",
number = "684",
publisher = "Springer-Verlag, Berlin",
address = "Padova, Italy",
editor = "A. Apostolico and M. Crochemore and Z. Galil and U. Manber",
pages = "74--86",
year = "1993",
url = "citeseer.ist.psu.edu/kannan93algorithm.html" }
Citations (may not include all citations):270 The String-to-String Correction Problem (context) - Wagner, Fischer - 1974
107 Quad-trees: a data structure for retrieval on composite key (context) - Finkel, Bentley - 1974
31 An algorithm for approximate tandem repeats - Landau, Schmidt - 1993
24 Efficient Parallel Algorithms for String Editing and Related.. (context) - Apostolico, Atallah et al. - 1990
18 Identification of common molecular sequences (context) - Smith, Waterman - 1981
16 An algorithm for locating non-overlapping regions of maximum.. - Kannan, Myers - 1993
4 An O(n log n) algorithm for finding all repetitions in a str.. (context) - Main, Lorentz - 1984
2 An algorithm for locating a repeated region (context) - Miller
2 A space efficient algorithm for finding the best non-overlap.. (context) - Benson - 1994
1 Binary codes of correcting deletions, insertions and reversa.. (context) - Levenshtein - 1966
1 An O(ND) difference algorithm and its variants (context) - Myers - 1986
The graph only includes citing articles where the year of publication is known.
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