Bit-parallel search algorithms for long patterns

Authors:
Branislav Ďurian;Hannu Peltola;Leena Salmela;Jorma Tarhio
Affiliations:
SST Slovakia s.r.o., Žilina, Slovakia;Department of Computer Science and Engineering, Aalto University, Aalto, Finland;Department of Computer Science, University of Helsinki, Finland;Department of Computer Science and Engineering, Aalto University, Aalto, Finland
Venue:
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
Year:
2010

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Abstract

We present three bit-parallel algorithms for exact searching of long patterns. Two algorithms are modifications of the BNDM algorithm and the third one is a filtration method which utilizes locations of q-grams in the pattern. Two algorithms apply a condensed representation of q-grams. Practical experiments show that the new algorithms are competitive with earlier algorithms with or without bit-parallelism. The average time complexity of the algorithms is analyzed. Two of the algorithms are shown to be optimal on average.