Sensitivity analysis and efficient method for identifying optimal spaced seeds

Please use this identifier to cite or link to this item: https://doi.org/10.1016/j.jcss.2003.04.002

Title:	Sensitivity analysis and efficient method for identifying optimal spaced seeds
Authors:	Choi, K.P. Zhang, L.
Keywords:	Filtration technique Heuristic algorithm Pattern matching Sensitivity analysis Sequence comparison Spaced seeds
Issue Date:	Feb-2004
Citation:	Choi, K.P., Zhang, L. (2004-02). Sensitivity analysis and efficient method for identifying optimal spaced seeds. Journal of Computer and System Sciences 68 (1) : 22-40. ScholarBank@NUS Repository. https://doi.org/10.1016/j.jcss.2003.04.002
Abstract:	The novel introduction of spaced seed idea in the filtration stage of sequence comparison by Ma et al. (Bioinformatics 18 (2002) 440) has greatly increased the sensitivity of homology search without compromising the speed of search. Finding the optimal spaced seeds is of great importance both theoretically and in designing better search tool for sequence comparison. In this paper, we study the computational aspects of calculating the hitting probability of spaced seeds; and based on these results, we propose an efficient algorithm for identifying optimal spaced seeds.
Source Title:	Journal of Computer and System Sciences
URI:	http://scholarbank.nus.edu.sg/handle/10635/104096
ISSN:	00220000
DOI:	10.1016/j.jcss.2003.04.002
Appears in Collections:	Staff Publications

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