Pattern matching with non overlapping reversals - Approximation and on-line algorithms

Amihood Amir, Benny Porat

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

The Sorting by Reversals Problem is known to be -hard. A simplification, Sorting by Signed Reversals is polynomially computable. Motivated by the Pattern Matching with Rearrangements model, we consider Pattern Matching with Reversals. Since this is a generalization of the Sorting by Reversals problem, it is clearly NP-hard. We, therefore consider the simplification where reversals cannot overlap. Such a constrained version has been researched in the past for various metrics in the rearrangement model - the swap metric and the interchange metric. We show that the constrained problem can be solved in linear time. We then consider the Approximate Pattern Matching with non-overlapping Reversals problem, i.e. where mismatch errors are introduced. We show that the problem can be solved in quadratic time and space. Finally, we consider the on-line version of the problem. We introduce a novel signature for palindromes and show that it has a pleasing behavior, similar to the Karp-Rabin signature. It allows solving the Pattern Matching with non-overlapping Reversals problem on-line in linear time w.h.p.

Original languageEnglish
Title of host publicationAlgorithms and Computation - 24th International Symposium, ISAAC 2013, Proceedings
Pages55-65
Number of pages11
DOIs
StatePublished - 2013
Event24th International Symposium on Algorithms and Computation, ISAAC 2013 - Hong Kong, China
Duration: 16 Dec 201318 Dec 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8283 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference24th International Symposium on Algorithms and Computation, ISAAC 2013
Country/TerritoryChina
CityHong Kong
Period16/12/1318/12/13

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