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Theoretical Computer Science
Volume 310, Issues 1-3, 1 January 2004, Pages 309-328
 
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doi:10.1016/S0304-3975(03)00423-7    How to Cite or Link Using DOI (Opens New Window)
Copyright © 2003 Elsevier B.V. All rights reserved.

Speeding up the detection of evolutive tandem repeats

Richard GroultCorresponding Author Contact Information, E-mail The Corresponding Author, a, 1, Martine LéonardE-mail The Corresponding Author, a and Laurent MouchardE-mail The Corresponding Author, b, c, 2

a LIFAR-ABISS, Faculté des Sciences, Universite de Rouen, 76821, Mont Saint Aignan, Cedex, France b UMR 6037-ABISS, Faculté des Sciences, Université de Rouen, 76821, Mont Saint Aignan, Cedex, France c Department Computer Science, King's College London, London WC2R 2LS, UK

Received 26 August 2002; 
revised 27 June 2003; 
accepted 28 July 2003;
Communicated by M. Crochemore 
Available online 15 August 2003.

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Abstract

We recently introduced evolutive tandem repeats with jump (using Hamming distance) (Proc. MFCS’02: the 27th Internat. Symp. Mathematical Foundations of Computer Science, Warszawa, Otwock, Poland, August 2002, Lecture Notes in Computer Science, Vol. 2420, Springer, Berlin, pp. 292–304) which consist in a series of almost contiguous copies having the following property: the Hamming distance between two consecutive copies is always smaller than a given parameter e. In this article, we present a significative improvement that speeds up the detection of evolutive tandem repeats. It is based on the progressive computation of distances between candidate copies participating to the evolutive tandem repeat. It leads to a new algorithm, still quadratic in the worst case, but much more efficient on average, authorizing larger sequences to be processed.

Author Keywords: Evolutive tandem repeats; Hamming distance; DNA sequences


 
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