High performance FPGA-based core for BLAST sequence alignment with the two-hit method

This paper presents the design and implementation of a high performance FPGA-based core for BLAST sequence alignment with the two-hit method. BLAST with two-hit is a very widely used heuristic biological sequence alignment algorithm, and this paper is the first reported FPGA implementation of it, to our knowledge. The architecture of our core is parameterized in terms of the 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 with the others. This results in a high performance and efficient FPGA implementation, which outperforms equivalent software implementations by one order of magnitude or more. Real hardware implementations show that our core is 52 times faster than equivalent software implementations, on average. 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 same code can be easily ported to different FPGA families and architectures.