Estimating seed sensitivity on homogeneous alignments

Details Estimating seed sensitivity on homogeneous alignments Estimating seed sensitivity on homogeneous alignments

2006-03-27

arxiv.org/abs/cs/0603106v1

Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE), 387-394, 2004

Computer Science

Other Computer Science

Scientific paper

10.1109/BIBE.2004.1317369

We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [18, 6, 3, 4, 10], 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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