Searching for a set of correlated patterns

Authors:
Shmuel T. Klein;Riva Shalom;Yair Kaufman
Affiliations:
Department of Computer Science, Bar Ilan University, Ramat-Gan 52900, Israel;Department of Computer Science, Bar Ilan University, Ramat-Gan 52900, Israel;Department of Computer Science, Bar Ilan University, Ramat-Gan 52900, Israel
Venue:
Journal of Discrete Algorithms
Year:
2007

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Abstract

New algorithms for searching simultaneously for a set of patterns in a text are suggested, for the special case where these patterns are correlated and have a common substring. This is then extended to the case where it could be more profitable to look for more than a single overlap, and a problem related to the generalization of this idea is shown to be NP-complete. Experimental results suggest that for this particular application, the suggested algorithm yields significant improvements over previous methods.