Pattern matching with address errors: Rearrangement distances

  • Authors:

  • Amihood Amir;Yonatan Aumann;Gary Benson;Avivit Levy;Ohad Lipsky;Ely Porat;Steven Skiena;Uzi Vishne

  • Affiliations:

  • Department of Computer Science, Bar-Ilan University, Ramat-Gan 52900, Israel and Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA;Department of Computer Science, Bar-Ilan University, Ramat-Gan 52900, Israel;Departments of Biology and Computer Science, Program in Bioinformatics, Boston University, Rm 207, 44 Cummington St., Boston, MA 02215, USA;Department of Computer Science, Bar-Ilan University, Ramat-Gan 52900, Israel;Department of Computer Science, Bar-Ilan University, Ramat-Gan 52900, Israel;Department of Computer Science, Bar-Ilan University, Ramat-Gan 52900, Israel;Department of Computer Science, State University of New York at Stony Brook, Stony Brook, NY 11794-4400, USA;Department of Mathematics, Bar-Ilan University, Ramat-Gan 52900, Israel

  • Venue:
  • Journal of Computer and System Sciences
  • Year:
  • 2009

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Abstract

Historically, approximate pattern matching has mainly focused at coping with errors in the data, while the order of the text/pattern was assumed to be more or less correct. In this paper we consider a class of pattern matching problems where the content is assumed to be correct, while the locations may have shifted/changed. We formally define a broad class of problems of this type, capturing situations in which the pattern is obtained from the text by a sequence of rearrangements. We consider several natural rearrangement schemes, including the analogues of the @?"1 and @?"2 distances, as well as two distances based on interchanges. For these, we present efficient algorithms to solve the resulting string matching problems.