Fast Computation of Good Multiple Spaced Seeds

Abstract

Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the further improvement provided by multiple spaced seeds in PatternHunterII, the sensitivity of dynamic programming is approached at BLASTn speed. Whereas computing optimal multiple spaced seeds was proved to be NP-hard, we show that, from practical point of view, computing good ones can be very efficient. We give a simple heuristic algorithm which computes good multiple seeds in polynomial time. Computing sensitivity is not required. When allowing the computation of the sensitivity for few seeds, we obtain better multiple seeds than previous ones in much shorter time.