Fast computation of a string duplication history under no-breakpoint-reuse

Brona Brejová; Martin Kravec; Gad M. Landau; Tomás Vinar

doi:10.1098/rsta.2013.0133

Fast computation of a string duplication history under no-breakpoint-reuse

Brona Brejová, Martin Kravec, Gad M. Landau, Tomás Vinar

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

Abstract

In this paper, we provide an O(n log2 n log log n log n) algorithm to compute a duplication history of a string under no-breakpoint-reuse condition. The motivation of this problem stems from computational biology, in particular, fromanalysis of complex gene clusters. The problem is also related to computing edit distance with block operations, but, in our scenario, the start of the history is not fixed, but chosen to minimize the distance measure.

Original language	English
Article number	20130133
Journal	Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Volume	372
DOIs	https://doi.org/10.1098/rsta.2013.0133
State	Published - 28 May 2014

Keywords

Duplication
Dynamic text
Edit distance
Sequence evolution

ASJC Scopus subject areas

General Mathematics
General Engineering
General Physics and Astronomy

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10.1098/rsta.2013.0133

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KW - Edit distance

KW - Sequence evolution

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Fast computation of a string duplication history under no-breakpoint-reuse

Abstract

Keywords

ASJC Scopus subject areas

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