Text matching with errors is a regular task in computational biology. We present an extension of the bit-parallel Wu-Manber algorithm [16] to combine several searches for a pattern into a collection of fixed-length words. We further present an OpenCL parallelization of a redundant index on massively parallel multicore processors, within a framework of searching for similarities with seed-based heuristics. We successfully implemented and ran our algorithms on GPU and multicore CPU. Some speedups obtained are more than 60×. © 2012 Springer-Verlag.
CITATION STYLE
Tran, T. T., Giraud, M., & Varré, J. S. (2012). Bit-parallel multiple pattern matching. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 7204 LNCS, pp. 292–301). https://doi.org/10.1007/978-3-642-31500-8_30
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