affiliation={Laboratoire d’Informatique Fondamentale de Lille – LIFL – CNRS : UMR8022 – INRIA – IRCICA – Universit{‘e} des Sciences et Technologies de Lille – Lille I – BONSAI – INRIA Lille – Nord Europe – CNRS : UMR8022 – Universit{‘e} des Sciences et Technologies de Lille – Lille I – INRIA},
Text matching with errors is a regular task in computational biology. We present an extension of the bit-parallel Wu-Manber algorithm 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 60x.
