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Design and Implementation of an FPGA-based Core for Gapped BLAST Sequence Alignment with the Two-Hit Method

This paper presents 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. This results in high performance and efficient FPGA implementations, which easily outperform equivalent software implementations by one order of magnitude or more. Furthermore, the core was captured in an FPGA-platform-independent language, namely the Handel-C language, to which no specific resource inference or placement constraints were applied. Hence, the core can be ported to different FPGA families and architectures.