Abstract
Optimized spaced seeds improve sensitivity and specificity in local homology search [1]. Recently, several authors [2-4] have shown that multiple seeds can have better sensitivity and specificity than single seeds. We describe a linear programming-based algorithm to optimize a set of seeds. Our algorithm offers a performance guarantee: the sensitivity of a chosen seed set is at least 70% of what can be achieved, in most reasonable models of homologous sequences. Our method achieves performance comparable to that of a greedy algorithm, but our work gives this area a mathematical foundation.
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Xu, J., Brown, D.G., Li, M., Ma, B. (2004). Optimizing Multiple Spaced Seeds for Homology Search. In: Sahinalp, S.C., Muthukrishnan, S., Dogrusoz, U. (eds) Combinatorial Pattern Matching. CPM 2004. Lecture Notes in Computer Science, vol 3109. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-27801-6_4
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DOI: https://doi.org/10.1007/978-3-540-27801-6_4
Publisher Name: Springer, Berlin, Heidelberg
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