Abstract
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×.
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Tran, T.T., Giraud, M., Varré, JS. (2012). Bit-Parallel Multiple Pattern Matching. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Waśniewski, J. (eds) Parallel Processing and Applied Mathematics. PPAM 2011. Lecture Notes in Computer Science, vol 7204. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31500-8_30
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DOI: https://doi.org/10.1007/978-3-642-31500-8_30
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