@inproceedings{b5a77be6ea4c4ff28f523f6a0b1a5e2b,

title = "New algorithms for the spaced seeds",

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′|2ML), where B′ is a subset of B; the second one improves the running time to O((M|B|) 2.236log(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.",

keywords = "Bioinformatics, Homology search, Spaced seed",

author = "Xin Gao and Li, {Shuai Cheng} and Yinan Lu",

year = "2007",

language = "English (US)",

isbn = "9783540738138",

volume = "4613 LNCS",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

pages = "50--61",

booktitle = "Frontiers in Algorithmics - First Annual International Workshop, FAW 2007, Proceedings",

note = "1st International Frontiers in Algorithmics Workshop, FAW 2007 ; Conference date: 01-08-2007 Through 03-08-2007",

}