Consensus optimizing both distance sum and radius

Amihood Amir, Gad M. Landau, Joong Chae Na, Heejin Park, Kunsoo Park, Jeong Seop Sim

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

Abstract

The consensus string problem is finding a representative string (consensus) of a given set of strings. In this paper we deal with the consensus string problems optimizing both distance sum and radius, where the distance sum is the sum of (Hamming) distances from the strings in to the consensus and the radius is the longest (Hamming) distance from the strings in to the consensus. Although there have been results considering either distance sum or radius, there have been no results considering both as far as we know. We present two algorithms to solve the consensus string problems optimizing both distance sum and radius for three strings. The first algorithm finds the optimal consensus string that minimizes both distance sum and radius, and the second algorithm finds the bounded consensus string such that, given constants s and r, the distance sum is at most s and the radius is at most r. Both algorithms take linear time.

Original languageEnglish
Title of host publicationString Processing and Information Retrieval - 16th International Symposium, SPIRE 2009, Proceedings
Pages234-242
Number of pages9
DOIs
StatePublished - 2009
Event16th International Symposium on String Processing and Information Retrieval, SPIRE 2009 - Saariselka, Finland
Duration: 25 Aug 200927 Aug 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5721 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference16th International Symposium on String Processing and Information Retrieval, SPIRE 2009
Country/TerritoryFinland
CitySaariselka
Period25/08/0927/08/09

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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