An improved algorithm for sequence comparison with block reversals

Shanmugavelayutham Muthukrishnan, S. Cenk Ṣahinalp

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    Given two sequences X and Y that are strings over some alphabet set, we consider the distance d(X, Y) between them defined to be minimum number of character replacements and block (substring) reversals needed to transform X to Y (or vice versa). This is the “simplest” sequence comparison problem we know of that allows natural block edit operations. Block reversals arise naturally in genomic sequence comparison; they are also of interest in matching music data. We present an improved algorithm for exactly computing the distance d(X, Y); it takes time O(|X| log2 |X|), and hence, is near-linear. Trivial approach takes quadratic time and the best known previous algorithm for this problem takes time Ω(|X| log3 |X|).

    Original languageEnglish (US)
    Title of host publicationLATIN 2002
    Subtitle of host publicationTheoretical Informatics - 5th Latin American Symposium, Proceedings
    EditorsSergio Rajsbaum
    PublisherSpringer-Verlag
    Pages319-325
    Number of pages7
    ISBN (Electronic)3540434003, 9783540434009
    StatePublished - Jan 1 2002
    Event5th Latin American Symposium on Theoretical Informatics, LATIN 2002 - Cancun, Mexico
    Duration: Apr 3 2002Apr 6 2002

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume2286
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Other

    Other5th Latin American Symposium on Theoretical Informatics, LATIN 2002
    CountryMexico
    CityCancun
    Period4/3/024/6/02

    Fingerprint

    Sequence Comparison
    Reversal
    Music
    Replacement
    Genomics
    Trivial
    Strings
    Transform
    Computing

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • Computer Science(all)

    Cite this

    Muthukrishnan, S., & Ṣahinalp, S. C. (2002). An improved algorithm for sequence comparison with block reversals. In S. Rajsbaum (Ed.), LATIN 2002: Theoretical Informatics - 5th Latin American Symposium, Proceedings (pp. 319-325). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2286). Springer-Verlag.

    An improved algorithm for sequence comparison with block reversals. / Muthukrishnan, Shanmugavelayutham; Ṣahinalp, S. Cenk.

    LATIN 2002: Theoretical Informatics - 5th Latin American Symposium, Proceedings. ed. / Sergio Rajsbaum. Springer-Verlag, 2002. p. 319-325 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2286).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Muthukrishnan, S & Ṣahinalp, SC 2002, An improved algorithm for sequence comparison with block reversals. in S Rajsbaum (ed.), LATIN 2002: Theoretical Informatics - 5th Latin American Symposium, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2286, Springer-Verlag, pp. 319-325, 5th Latin American Symposium on Theoretical Informatics, LATIN 2002, Cancun, Mexico, 4/3/02.
    Muthukrishnan S, Ṣahinalp SC. An improved algorithm for sequence comparison with block reversals. In Rajsbaum S, editor, LATIN 2002: Theoretical Informatics - 5th Latin American Symposium, Proceedings. Springer-Verlag. 2002. p. 319-325. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
    Muthukrishnan, Shanmugavelayutham ; Ṣahinalp, S. Cenk. / An improved algorithm for sequence comparison with block reversals. LATIN 2002: Theoretical Informatics - 5th Latin American Symposium, Proceedings. editor / Sergio Rajsbaum. Springer-Verlag, 2002. pp. 319-325 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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