Abstract
The best known algorithm computes the sensitivity of a given spaced seed on a random region with running time O((M + L)|B|), where M is the length of the seed, L is the length of the random region, and |B| is the size of seed-compatible-suffix set, which is exponential to the number of 0’s in the seed. We developed two algorithms to improve this running time: the first one improves the running time to O(|B′|2 ML), where B′ is a subset of B; the second one improves the running time to O((M|B|)2.236 log(L/M)), which will be much smaller than the original running time when L is large. We also developed a Monte Carlo algorithm which can guarantee to quickly find a near optimal seed with high probability.
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Gao, X., Li, S.C., Lu, Y. (2007). New Algorithms for the Spaced Seeds. In: Preparata, F.P., Fang, Q. (eds) Frontiers in Algorithmics. FAW 2007. Lecture Notes in Computer Science, vol 4613. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73814-5_5
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DOI: https://doi.org/10.1007/978-3-540-73814-5_5
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