Two Algorithms for LCS Consecutive Suffix Alignment

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

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-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 languageEnglish
Title of host publicationCombinatorial Pattern Matching
Subtitle of host publicationProceedings of the 15th Annual Symposium, CPM 2004
EditorsSuleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusoz
PublisherSpringer Verlag
Pages173-193
Number of pages21
ISBN (Print)354022341X, 9783540223412
DOIs
StatePublished - 1 Jan 2004
Externally publishedYes
Event15th Annual Symposium on Combinatorial Pattern Matching - Istanbul, Turkey
Duration: 5 Jul 20047 Jul 2004

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3109

Conference

Conference15th Annual Symposium on Combinatorial Pattern Matching
Abbreviated titleCPM 2004
Country/TerritoryTurkey
CityIstanbul
Period5/07/047/07/04

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