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Finding approximate repetitions under Hamming distance

Roman Kolpakov 1 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 tandem repetitions 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 ($S$ the size of the output). This improves, in particular, the bound obtained in \citeLS93. Finally, other possible definions are briefly analyzed.}
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https://hal.inria.fr/inria-00072459
Contributor : Rapport de Recherche Inria <>
Submitted on : Wednesday, May 24, 2006 - 10:01:09 AM
Last modification on : Friday, February 26, 2021 - 3:28:02 PM
Long-term archiving on: : Sunday, April 4, 2010 - 11:08:39 PM

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  • HAL Id : inria-00072459, version 1

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Roman Kolpakov, Gregory Kucherov. Finding approximate repetitions under Hamming distance. [Research Report] RR-4163, INRIA. 2001, pp.30. ⟨inria-00072459⟩

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