cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

BLAST, short for Basic Local Alignment Search Tool, is a fundamental algorithm in the life sciences that compares biological sequences [1.2]. With the advent of next-generation sequencing (NGS), the exponential growth of sequence databases is arguably outstripping our ability to analyze the data. The previous studies [3.4.5.6] for accelerating BLAST on GPU used coarse-grained parallel approaches, (i.e. one sequence alignment is mapped to only one thread), which are not adapted to GPU architecture and cannot solve the irregular memory access in BLAST. Our goal is to propose a faster GPU-BLAST using the fine-grained multithreaded approach