Parallel implementation of the Wu-Manber algorithm using the OpenCL framework

Abstract

One of the most significant issues of the computational biology is the multiple pattern matching for locating nucleotides and amino acid sequence patterns into biological databases. Sequential implementations for these processes have become inadequate, due to an increasing demand for more computational power. Graphic cards offer a high parallelism computational power improving the performance of applications. This paper evaluates the performance of the Wu-Manber algorithm implemented with the OpenCL framework, by presenting the running time of the experiments compared with the corresponding sequential time. © 2012 IFIP International Federation for Information Processing.