BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware …

This work has: •Examined, compared and evaluated 22 programming languages and environments for parallel computing on multi-core CPUs and GPUs •Chosen to use OpenMP as the standard for multi-core CPU programming and OpenCL for GPU programming •Re-implemented a number of standard and well-known algorithms …