Fast computation of a string duplication history under no-breakpoint-reuse (extended abstract)

Broňa Brejová, Gad M. Landau, Tomáš Vinař

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

Abstract

In this paper, we provide an O(n log2 n log log n log* n) algorithm to compute a duplication history of a string under no-breakpoint-reuse condition. Our algorithm is an efficient implementation of earlier work by Zhang et al. (2009). The motivation of this problem stems from computational biology, in particular from analysis of complex gene clusters. The problem is also related to computing edit distance with block operations, but in our scenario the start of the history is not fixed, but chosen to minimize the distance measure.

Original languageEnglish
Title of host publicationString Processing and Information Retrieval - 18th International Symposium, SPIRE 2011, Proceedings
Pages144-155
Number of pages12
DOIs
StatePublished - 2011
Event18th International Symposium on String Processing and Information Retrieval, SPIRE 2011 - Pisa, Italy
Duration: 17 Oct 201121 Oct 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7024 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference18th International Symposium on String Processing and Information Retrieval, SPIRE 2011
Country/TerritoryItaly
CityPisa
Period17/10/1121/10/11

Keywords

  • duplication
  • dynamic text
  • edit distance
  • sequence evolution

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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