Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits.
Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis.
Citation: Chikkagoudar, S., Wang, K., & Li, M. (2011). GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores. BMC research notes, 4(1), 158.
This program stopped working at CUDA 5.0 and has not been updated. It is a shame because this might be a very useful program. Someone please update it. I do not have the expertise to do this. BTW, to all developers - please consider your program name and make it unique so it is easily googled! I wish the developers of R had done so - have you ever tried to google "R"?