Optimal spaced seeds for faster approximate string matching

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

    Research output: Contribution to journalConference articlepeer-review


    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. don't 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 optimally design spaced seeds that yield no false negatives.

    Original languageEnglish (US)
    Pages (from-to)1251-1262
    Number of pages12
    JournalLecture Notes in Computer Science
    StatePublished - 2005
    Event32nd International Colloquium on Automata, Languages and Programming, ICALP 2005 - Lisbon, Portugal
    Duration: Jul 11 2005Jul 15 2005

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • General Computer Science


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