BLAZE: Exploiting Hybrid Parallelism and Size-customized Kernels to Accelerate BLASTP on GPUs

Basic Local Alignment Search Tool (BLAST/BLASTP) [3], often referred to as the Google of biological research [9], is widely used to query a large database to find homologous gene/protein sequences. Though there have been attempts to accelerate BLASTP, the protein sequence alignment tool, on GPUs, they remain slower than CPU/multicore-based multi-threaded implementations. In this paper, we introduce BLAZE, a GPU-accelerated drop-in replacement for BLASTP that produces identical results while achieving speedups over both multithreaded and GPU-accelerated implementations.