An efficient algorithm for sequence comparison with block reversals

S. Muthukrishnan, S. Cenk Sahinalp

    Research output: Contribution to journalConference articlepeer-review


    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). The operations are required to be disjoint. 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 algorithm for exactly computing the distance d(X,Y); it takes time O(|X|log 2|X|), and hence, is near-linear. Trivial approach takes quadratic time.

    Original languageEnglish (US)
    Pages (from-to)95-101
    Number of pages7
    JournalTheoretical Computer Science
    Issue number1
    StatePublished - Jun 16 2004
    EventLatin American Theoretical Informatics - Cancun, Mexico
    Duration: Apr 3 2002Apr 6 2002


    • Block edit distance
    • Sequence comparison
    • String periodicity

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • General Computer Science


    Dive into the research topics of 'An efficient algorithm for sequence comparison with block reversals'. Together they form a unique fingerprint.

    Cite this