External Memory Algorithms for String Problems

  • Authors:

  • Kangho Roh;Maxime Crochemore;Costas S. Iliopoulos;Kunsoo Park

  • Affiliations:

  • School of Computer Science and Engineering, Seoul National University, Seoul, Korea. E-mail: {khroh,kpark}@theory.snu.ac.kr;Dept. of Computer Sciences, King's College London, UK and Université Paris-Est, France. E-mail: Maxime.Crochemore@kcl.ac.uk;Department of Computer Sciences, King's College London, London, United Kingdom. E-mail: csi@dcs.kcl.ac.uk;School of Computer Science and Engineering, Seoul National University, Seoul, Korea. E-mail: {khroh,kpark}@theory.snu.ac.kr

  • Venue:
  • Fundamenta Informaticae - Workshop on Combinatorial Algorithms
  • Year:
  • 2008

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Abstract

In this paper we present external memory algorithms for some string problems. External memory algorithms have been developed in many research areas, as the speed gap between fast internal memory and slow external memory continues to grow. The goal of external memory algorithms is to minimize the number of input/output operations between internal memory and external memory. These years the sizes of strings such as DNA sequences are rapidly increasing. However, external memory algorithms have been developed for only a few string problems. In this paper we consider five string problems and present external memory algorithms for them. They are the problems of finding the maximum suffix, string matching, period finding, Lyndon decomposition, and finding the minimum of a circular string. Every algorithm that we present here runs in a linear number of I/Os in the external memory model with one disk, and they run in an optimal number of disk I/Os in the external memory model with multiple disks.