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.

Recognizing the importance of whole genome alignment (WGA), the National Institutes for Health maintains LASTZ, a sequential WGA application. As genomic data grows, there is a compelling need for scalable, high-performance WGA. Unfortunately, high-sensitivity, `gapped' alignment which uses dynamic programming (DP) is slow, whereas faster alignment with ungapped filtering is often less sensitive. We develop FastZ, a GPU-accelerated, gapped WGA software which matches gapped LASTZ in sensitivity. FastZ employs a novel inspector-executor scheme in which (a) the lightweight inspector elides DP traceback except in common, extremely short alignments, where the inspector performs limited, eager traceback to eliminate the executor, and (b) executor trimming avoids unnecessary work. Further, FastZ employs register-based cyclic-buffering to drastically reduce memory traffic, and groups DP problems by size for load balance. FastZ running on an RTX 3080 GPU and our multicore implementation of LASTZ achieve 111x and 20x speedups over the sequential LASTZ, respectively.