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Reports (Research Report) Year : 2003

Estimating seed sensitivity on homogeneous alignments

Laurent Noé
Yann Ponty


We address the problem of measuring the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models, we study the measurement based on homogeneous alignments. We describe an algorithm for counting and random generation of those alignments and an algorithm for exact computation of the sensitivity for a broad class of seed strategies. We provide experimental results demonstrating a bias introduced by ignoring the homogeneousness condition.
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Dates and versions

inria-00071536 , version 1 (23-05-2006)


  • HAL Id : inria-00071536 , version 1


Gregory Kucherov, Laurent Noé, Yann Ponty. Estimating seed sensitivity on homogeneous alignments. [Research Report] RR-5047, INRIA. 2003, pp.17. ⟨inria-00071536⟩
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