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An Improved Algorithm for Sequence Comparison with Block Reversals

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Book cover LATIN 2002: Theoretical Informatics (LATIN 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2286))

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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).

Supported in part by a grant from Charles B. Wang foundation.

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Author information

Authors and Affiliations

  1. AT& T Labs - Research, 180 Park Avenue, 07932, Florham Park, NJ, USA

    S. Muthukrishnan

  2. Dept of EECS, Dept of Genetics, and Cntr for Computational Genomics, Case Western Reserve University, 44106, Cleveland, OH, USA

    S. Cenk Sahinalp

Authors
  1. S. Muthukrishnan
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  2. S. Cenk Sahinalp
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Editor information

Editors and Affiliations

  1. Compaq Cambridge Research Laboratory, One Cambridge Center, 02142-1612, Cambridge, MA, USA

    Sergio Rajsbaum

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© 2002 Springer-Verlag Berlin Heidelberg

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Muthukrishnan, S., Sahinalp, S.C. (2002). An Improved Algorithm for Sequence Comparison with Block Reversals. In: Rajsbaum, S. (eds) LATIN 2002: Theoretical Informatics. LATIN 2002. Lecture Notes in Computer Science, vol 2286. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45995-2_30

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  • DOI: https://doi.org/10.1007/3-540-45995-2_30

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43400-9

  • Online ISBN: 978-3-540-45995-8

  • eBook Packages: Springer Book Archive

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