University of Economics, Prague
In this paper, the authors present the design and implementation of the first FPGA-based core for Gapped BLAST sequence alignment with the two-hit method, ever reported in the literature. Gapped BLAST with two hit is a heuristic biological sequence alignment algorithm which is very widely used in the bioinformatics and computational biology world. The architecture of the core is parameterized in terms of sequence lengths, match scores, gap penalties and cut-off, and threshold values. It is composed of various blocks each of which performs one step of the algorithm in parallel.