Tuning approximate Boyer-Moore for gene sequences

Authors:
Petri Kalsi;Leena Salmela;Jorma Tarhio
Affiliations:
Helsinki University of Technology;Helsinki University of Technology;Helsinki University of Technology
Venue:
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
Year:
2007

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Abstract

Recently a new variation of approximate Boyer-Moore string matching was presented for the k-mismatch problem. This variation was developed for gene sequences. We further tuned this algorithm gaining speedups in both preprocessing and search times. Our preprocessing has lower time complexity than the previous algorithm and our experiments show that our algorithm is over 30% faster than the previous one. We also present two variations of the algorithm for the k-difference problem.