Two Algorithms for LCS Consecutive Suffix Alignment

Gad M. Landau; Eugene Myers; Michal Ziv-Ukelson

doi:10.1007/978-3-540-27801-6_13

Two Algorithms for LCS Consecutive Suffix Alignment

Gad M. Landau, Eugene Myers, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

14 Scopus citations

Abstract

The problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B. Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS metric. The first solution is an O(nL) time and space algorithm for constant alphabets, where n is the size of the compared strings and L < n denotes the size of the LCS of A and B. The second solution is an O(nL + n log |∑|) time and O(L) space algorithm for general alphabets, where S denotes the alphabet of the compared strings. (Note that \∑\ < n.)

Original language	English
Title of host publication	Combinatorial Pattern Matching
Subtitle of host publication	Proceedings of the 15th Annual Symposium, CPM 2004
Editors	Suleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusoz
Publisher	Springer Verlag
Pages	173-193
Number of pages	21
ISBN (Print)	354022341X, 9783540223412
DOIs	https://doi.org/10.1007/978-3-540-27801-6_13
State	Published - 1 Jan 2004
Externally published	Yes
Event	15th Annual Symposium on Combinatorial Pattern Matching - Istanbul, Turkey Duration: 5 Jul 2004 → 7 Jul 2004

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	3109

Conference

Conference	15th Annual Symposium on Combinatorial Pattern Matching
Abbreviated title	CPM 2004
Country/Territory	Turkey
City	Istanbul
Period	5/07/04 → 7/07/04

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10.1007/978-3-540-27801-6_13

Cite this

Landau, G. M., Myers, E., & Ziv-Ukelson, M. (2004). Two Algorithms for LCS Consecutive Suffix Alignment. In S. C. Sahinalp, S. Muthukrishnan, & U. Dogrusoz (Eds.), Combinatorial Pattern Matching: Proceedings of the 15th Annual Symposium, CPM 2004 (pp. 173-193). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3109). Springer Verlag. https://doi.org/10.1007/978-3-540-27801-6_13

Landau, Gad M. ; Myers, Eugene ; Ziv-Ukelson, Michal. / Two Algorithms for LCS Consecutive Suffix Alignment. Combinatorial Pattern Matching: Proceedings of the 15th Annual Symposium, CPM 2004. editor / Suleyman Cenk Sahinalp ; S. Muthukrishnan ; Ugur Dogrusoz. Springer Verlag, 2004. pp. 173-193 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "The problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B. Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS metric. The first solution is an O(nL) time and space algorithm for constant alphabets, where n is the size of the compared strings and L < n denotes the size of the LCS of A and B. The second solution is an O(nL + n log |∑|) time and O(L) space algorithm for general alphabets, where S denotes the alphabet of the compared strings. (Note that \∑\ < n.)",

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Landau, GM, Myers, E & Ziv-Ukelson, M 2004, Two Algorithms for LCS Consecutive Suffix Alignment. in SC Sahinalp, S Muthukrishnan & U Dogrusoz (eds), Combinatorial Pattern Matching: Proceedings of the 15th Annual Symposium, CPM 2004. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3109, Springer Verlag, pp. 173-193, 15th Annual Symposium on Combinatorial Pattern Matching, Istanbul, Turkey, 5/07/04. https://doi.org/10.1007/978-3-540-27801-6_13

Two Algorithms for LCS Consecutive Suffix Alignment. / Landau, Gad M.; Myers, Eugene; Ziv-Ukelson, Michal.

Combinatorial Pattern Matching: Proceedings of the 15th Annual Symposium, CPM 2004. ed. / Suleyman Cenk Sahinalp; S. Muthukrishnan; Ugur Dogrusoz. Springer Verlag, 2004. p. 173-193 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3109).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Y1 - 2004/1/1

N2 - The problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B. Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS metric. The first solution is an O(nL) time and space algorithm for constant alphabets, where n is the size of the compared strings and L < n denotes the size of the LCS of A and B. The second solution is an O(nL + n log |∑|) time and O(L) space algorithm for general alphabets, where S denotes the alphabet of the compared strings. (Note that \∑\ < n.)

AB - The problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B. Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS metric. The first solution is an O(nL) time and space algorithm for constant alphabets, where n is the size of the compared strings and L < n denotes the size of the LCS of A and B. The second solution is an O(nL + n log |∑|) time and O(L) space algorithm for general alphabets, where S denotes the alphabet of the compared strings. (Note that \∑\ < n.)

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T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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Landau GM, Myers E, Ziv-Ukelson M. Two Algorithms for LCS Consecutive Suffix Alignment. In Sahinalp SC, Muthukrishnan S, Dogrusoz U, editors, Combinatorial Pattern Matching: Proceedings of the 15th Annual Symposium, CPM 2004. Springer Verlag. 2004. p. 173-193. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-540-27801-6_13

Two Algorithms for LCS Consecutive Suffix Alignment

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