Efficient CUDA code for pairwise local alignment of two sequences. Use makefile to compile the code. To execute type : mpirun SW_exe argument1 argument2
argument1: size of the subject sequence,
argument2: size of the query sequence
The algorithm implemented by this codebase is described in the following peer-reviewed publication. Please cite this paper, when using our code for academic purposes:
Chirag Jain, Subodh Kumar. "Fine-grained GPU parallelization of pairwise local sequence alignment" High Performance Computing (HiPC), 2014 21st International Conference on. IEEE, 2014.
