Fast and simple computations using prefix tables under hamming and edit distance

C. Barton, Costas Iliopoulos, S.P. Pissis, W.F. Smyth

    Research output: Chapter in Book/Conference paperConference paper

    4 Citations (Scopus)

    Abstract

    © Springer International Publishing Switzerland 2015. In this article, we introduce a new and simple data structure, the prefix table under Hamming distance, and present two algorithms to compute it efficiently: one asymptotically fast; the other very fast on average and in practice. Because the latter approach avoids the computation of global data structures, such as the suffix array and the longest common prefix array, it yields algorithms much faster in practice than existing methods. We show how this data structure can be used to solve two string problems of interest: (a) approximate string matching under Hamming distance; and (b) longest approximate overlap under Hamming distance. Analogously, we introduce the prefix table under edit distance, and present an efficient algorithm for its computation. In the process, we also define the border array under both distance measures, and provide an algorithm for conversion between prefix tables and border arrays.
    Original languageEnglish
    Title of host publicationCombinatorial Algorithms
    Place of PublicationUSA
    PublisherSpringer
    Pages49-61
    Volume8986
    ISBN (Print)9783319193144
    DOIs
    Publication statusPublished - 2015
    Event25th International Workshop on Combinatorial Algorithms 2014 - Duluth, United States
    Duration: 15 Oct 201417 Dec 2014

    Conference

    Conference25th International Workshop on Combinatorial Algorithms 2014
    Abbreviated titleIWOCA 2014
    CountryUnited States
    CityDuluth
    Period15/10/1417/12/14

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