Optimal spaced seeds for faster approximate string matching

Martin Farach-Colton, Gad M. Landau, S. Cenk Sahinalp, Dekel Tsur

Research output: Contribution to journalArticlepeer-review

Abstract

Filtering is a standard technique for fast approximate string matching in practice. In filtering, a quick first step is used to rule out almost all positions of a text as possible starting positions for a pattern. Typically this step consists of finding the exact matches of small parts of the pattern. In the followup step, a slow method is used to verify or eliminate each remaining position. The running time of such a method depends largely on the quality of the filtering step, as measured by its false positives rate. The quality of such a method depends on the number of true matches that it misses, that is, on its false negative rate. A spaced seed is a recently introduced type of filter pattern that allows gaps (i.e. do not cares) in the small sub-pattern to be searched for. Spaced seeds promise to yield a much lower false positives rate, and thus have been extensively studied, though heretofore only heuristically or statistically. In this paper, we show how to design almost optimal spaced seeds that yield no false negatives.

Original languageEnglish
Pages (from-to)1035-1044
Number of pages10
JournalJournal of Computer and System Sciences
Volume73
Issue number7
DOIs
StatePublished - Nov 2007

Keywords

  • Hamming distance
  • Pattern matching
  • Seeds design

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Applied Mathematics
  • General Computer Science
  • Computer Networks and Communications
  • Computational Theory and Mathematics

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