Optimization of DNA Sequences Data to Accelerate DNA Sequence Alignment on FPGA

This paper presents the design and development of high performance accelerating and optimization technique for accelerate the process of DNA sequences alignment. The scope of the paper focuses on memory and speed optimization by optimizing and mapping the DNA sequences data before alignment. This optimization technique is designed based on novel data compression technique in optimizing the numbers of data transmitted from computer to DNA sequences alignment accelerator. Consequently, the numbers of data per serial data transmission for alignment can be optimize and accelerate up to 400% greater than conventional DNA sequences alignment accelerator system. This technique has been design and implemented on hardware based acceleration device and targeted to Altera Cyclone II 2C70 FPGA and using 50 MHz oscillator for clock source. The code is written in verilog HDL syntax using Quartus 2 version 7.2 and the simulation is verified using Quartus 2 version 7.2 simulator tools. As a result, the theoretical analysis, simulation and implementation result based on development and implementation of the proposed design on FPGA are presented and well organized in this paper. The comparative study based on theoretical, simulation and implementation results of this technique has been made to accomplish result of analysis.