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13th IEEE International Conference on BioInformatics and BioEngineering (2004)
Taichung, Taiwan, ROC
May 19, 2004 to May 21, 2004
ISBN: 0-7695-2173-8
pp: 387
Gregory Kucherov , LORIA/INRIA-Lorraine, France
Laurent Noé , LORIA/INRIA-Lorraine, France
Yann Ponty , LRI, France
We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [Faster and more sensitive homology search, Designing seeds for similarity search in genomic DNA, Optimal spaced seeds for Hidden Markov Models, with application to homologous coding regions, Vector seeds: an extension to spaced seeds allows substantial improvements in sensitivity and specificity, Sensitivity analysis and efficient method for identifying optimal spaced seeds], we study the estimation 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.

L. Noé, G. Kucherov and Y. Ponty, "Estimating Seed Sensitivity on Homogeneous Alignments," 13th IEEE International Conference on BioInformatics and BioEngineering(BIBE), Taichung, Taiwan, ROC, 2004, pp. 387.
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