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Published Articles >> Table of Contents >> Abstract
Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04)
p. 387
Estimating Seed Sensitivity on Homogeneous Alignments
Gregory Kucherov, LORIA/INRIA-Lorraine, France
Laurent Noe, LORIA/INRIA-Lorraine, France
Yann Ponty, LRI, France
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DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/BIBE.2004.1317369
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| Abstract |
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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.
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Citation:
Gregory Kucherov, Laurent Noe, Yann Ponty,
"Estimating Seed Sensitivity on Homogeneous Alignments,"
bibe,
p. 387,
Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04),
2004
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