Finding approximate repetitions under Hamming distance

Roman Kolpakov Gregory Kucherov 1
1 ADAGE - Applying discrete algorithms to genomics
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : The problem of computing periodicities with $K$ possible mismatches is studied. Two main definitions are considered, and for both of them an $O(nK\log K+S)$ algorithm is proposed ($n$ the word length and $S$ the size of the output). This improves, in particular, the bound obtained in \cite{LS93}. Finally, other possible definitions are briefly analyzed.
Type de document :
Article dans une revue
Theoretical Computer Science, Elsevier, 2003, 303 (1), pp.135-156
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https://hal.inria.fr/inria-00099592
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Soumis le : mardi 26 septembre 2006 - 09:39:07
Dernière modification le : jeudi 17 mai 2018 - 12:52:03

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  • HAL Id : inria-00099592, version 1

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Roman Kolpakov, Gregory Kucherov. Finding approximate repetitions under Hamming distance. Theoretical Computer Science, Elsevier, 2003, 303 (1), pp.135-156. 〈inria-00099592〉

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