### 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| log^{2} |X|), and hence, is near-linear. Trivial approach takes quadratic time and the best known previous algorithm for this problem takes time Ω(|X| log^{3} |X|).

Original language | English (US) |
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Title of host publication | LATIN 2002 |

Subtitle of host publication | Theoretical Informatics - 5th Latin American Symposium, Proceedings |

Editors | Sergio Rajsbaum |

Publisher | Springer-Verlag |

Pages | 319-325 |

Number of pages | 7 |

ISBN (Electronic) | 3540434003, 9783540434009 |

State | Published - Jan 1 2002 |

Event | 5th Latin American Symposium on Theoretical Informatics, LATIN 2002 - Cancun, Mexico Duration: Apr 3 2002 → Apr 6 2002 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 2286 |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 5th Latin American Symposium on Theoretical Informatics, LATIN 2002 |
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Country | Mexico |

City | Cancun |

Period | 4/3/02 → 4/6/02 |

### Fingerprint

### ASJC Scopus subject areas

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*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.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

*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.

}

TY - GEN

T1 - An improved algorithm for sequence comparison with block reversals

AU - Muthukrishnan, Shanmugavelayutham

AU - Ṣahinalp, S. Cenk

PY - 2002/1/1

Y1 - 2002/1/1

N2 - 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|).

AB - 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|).

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UR - http://www.scopus.com/inward/citedby.url?scp=84937412871&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:84937412871

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 319

EP - 325

BT - LATIN 2002

A2 - Rajsbaum, Sergio

PB - Springer-Verlag

ER -