FPGA-Based Hardware Architecture for Sequence Alignment by Genetic Algorithm

With the advent of next-gen DNA sequencing technologies, there has been a massive growth in sequencing data and demand for analysis. The sequence of macromolecules such as DNA, RNA, and proteins are fundamental to the study of biology and medicine. Among many multiple sequence alignment techniques, Sequence Alignment by Genetic Algorithm (SAGA) generates high-quality alignments, but is computationally intensive, leading to low performance. In this paper, we propose an FPGA-based hardware architecture for SAGA to address the complexity and performance issues of SAGA.