CUDA-MEME

mCUDA-MEME is a well-established ultrafast scalable motif discovery algorithm based on MEME (version 4.4.0) algorithm for multiple GPUs using a hybrid combination of CUDA, MPI and OpenMP parallel programming models. This algorithm is a further extension of CUDA-MEME (based on MEME version 3.5.4) with respect to accuracy and speed and has been tested on a GPU cluster with eight compute nodes and two Fermi-based Tesla S2050 (and Tesla-based Tesla S1070) quad-GPU computing systems, running the Linux OS with the MPICH2 library. The experimental results showed that our algorithm scales well with respect to both dataset sizes and the number of GPUs. At present, OOPS and ZOOPS models are supported, which are sufficient for most motif discovery applications. In addtion, this algorithm has been incorporated to NVIDIA Tesla Bio Workbench and deployed in NIH Biowulf.