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Journal articles

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.
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Submitted on : Tuesday, September 26, 2006 - 9:39:07 AM
Last modification on : Friday, February 4, 2022 - 3:30:55 AM


  • HAL Id : inria-00099592, version 1



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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