Fast string matching for DNA sequences

Abstract In this paper we propose the Maximal Average Shift (MAS) algorithm that finds a pattern scan order that maximizes the average shift length. We also present two extensions of MAS: one improves the scan speed of MAS by using the scan result of the previous window, and the other improves the running time of MAS by using q-grams. These algorithms show better average performances in scan speed than previous string matching algorithms for DNA sequences.

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