DOPA: GPU-based protein alignment using database and memory access optimizations

摘要

BackgroundSmith-Waterman (S-W) algorithm is an optimal sequence alignment method for biological databases, but its computational complexity makes it too slow for practical purposes. Heuristics based approximate methods like FASTA and BLAST provide faster solutions but at the cost of reduced accuracy. Also, the expanding volume and varying lengths of sequences necessitate performance efficient restructuring of these databases. Thus to come up with an accurate and fast solution, it is highly desired to speed up the S-W algorithm.