### 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). 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 language | English (US) |
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Pages (from-to) | 95-101 |

Number of pages | 7 |

Journal | Theoretical Computer Science |

Volume | 321 |

Issue number | 1 |

DOIs | |

State | Published - Jun 16 2004 |

Event | Latin American Theoretical Informatics - Cancun, Mexico Duration: Apr 3 2002 → Apr 6 2002 |

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### Keywords

- Block edit distance
- Sequence comparison
- String periodicity

### ASJC Scopus subject areas

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*Theoretical Computer Science*,

*321*(1), 95-101. https://doi.org/10.1016/j.tcs.2003.05.005

**An efficient algorithm for sequence comparison with block reversals.** / Muthukrishnan, Shanmugavelayutham; Sahinalp, S. Cenk.

Research output: Contribution to journal › Conference article

*Theoretical Computer Science*, vol. 321, no. 1, pp. 95-101. https://doi.org/10.1016/j.tcs.2003.05.005

}

TY - JOUR

T1 - An efficient algorithm for sequence comparison with block reversals

AU - Muthukrishnan, Shanmugavelayutham

AU - Sahinalp, S. Cenk

PY - 2004/6/16

Y1 - 2004/6/16

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). 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.

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). 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.

KW - Block edit distance

KW - Sequence comparison

KW - String periodicity

UR - http://www.scopus.com/inward/record.url?scp=2442543058&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=2442543058&partnerID=8YFLogxK

U2 - 10.1016/j.tcs.2003.05.005

DO - 10.1016/j.tcs.2003.05.005

M3 - Conference article

AN - SCOPUS:2442543058

VL - 321

SP - 95

EP - 101

JO - Theoretical Computer Science

JF - Theoretical Computer Science

SN - 0304-3975

IS - 1

ER -