FPGA Implementation of DNA Sequence Alignment with Traceback

An FPGA-based improved sequence alignment architecture is introduced in this manuscript. This paper clearly expresses a straightforward design of the hardware architecture of sequence alignment in FPGA for pair-wise global alignment technique to achieve the necessity of high-throughput processing. Moreover, this architecture is working in a well-organized and competent manner. It utilizes the resources available in FPGA to improve the actual time of the alignment process to align sequences by utilizing only few digital logic circuitry for primitive operations sequentially. This FPGA-based architecture design is synthesised for several cases taking into account of different length of pseudo randomly generated sequences. The proposed design provides sequence alignment with similarity score of the sequences which leads to close similarity between the sequences. Simulation results indicate that the proposed approach consumes reasonably low FPGA resources in implementing the architecture.