Hotspot Analysis Based Partial CUDA Acceleration of HMMER 3.0 on GPGPUs
With the introduction of many-core GPUs, there is widespread interest in using GPUs to accelerate non-graphics applications such as bioinformatics, energy, finance and several research areas. Even though the GPUs provide highly parallel processing capability, the communication interface between CPU and GPU could be a performance bottleneck due to heavy data transfer. If data transfer time is overwhelming the computation time on GPU, it would be better keep the computation on CPU instead of using GPUs. In this paper, the authors characterize the HMMER 3.0 and investigate performance hotspot functions. The HMMER is a bioinformatics application which is used in searching sequence databases for protein sequences.