In the shortest common superstring problem (SCS) one is given a set s 1,..., sn of n strings and the goal is to find a shortest string containing each si as a substring. While many approximation algorithms for this problem have been developed, it is still not known whether it can be solved exactly in fewer than 2n steps. In this paper we present an algorithm that solves the special case when all of the input strings have length 3 in time 3n/3 and polynomial space. The algorithm generates a combination of a de Bruijn graph and an overlap graph, such that a SCS is then a shortest directed rural postman path (DRPP) on this graph. We show that there exists at least one optimal DRPP satisfying some natural properties. The algorithm works basically by exhaustive search, but on the reduced search space of such paths of size 3n/3.

Original languageEnglish
Title of host publicationMathematical Foundations of Computer Science 2013 - 38th International Symposium, MFCS 2013, Proceedings
Pages480-491
Number of pages12
DOIs
StatePublished - 15 Oct 2013
Event38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013 - Klosterneuburg, Austria
Duration: 26 Aug 201330 Aug 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8087 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013
Country/TerritoryAustria
CityKlosterneuburg
Period26/08/1330/08/13

    Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

ID: 49826082