Accelerating DNA Sequence Alignment using Altera DE2-115

Abstract

DNA sequence alignment is a technique for discovering information between two base sequences which the Smith-Waterman algorithm is the accurate method that provides a precise result for alignment compared to others. However, the performance was influence by size of dataset and a long DNA base sequence which resulted the time required for the alignment process is much longer in relation to the number of DNA sequence samples. There are many ways to accelerate DNA sequence alignment, and Field Programmable Gate Array (FPGA) is a good choice due to its parallel processing and cost efficiency. Although FPGA acceleration approaches are not new, this work investigates a purely software-based FPGA acceleration using the Altera Cyclone IV EP4CE115F29C7N FPGA as the target device. The SW algorithm was developed using the C language in Quartus II version 18.1 and the Nios II software build tools for Eclipse. The development starts with setting up the Qsys architecture before developing the code in Eclipse to determine the computational performance. The result shows the computational timing and speed of the implementation, with the highest speed achieved being 198.76 cells per millisecond. To summarise, the computational performance ultimately depends on the maximum matrix size of the FPGA, which is also influenced by the DNA-based pair length and able to complete using low-cost FPGA.