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This paper presents the development of high performance accelerating technique for DNA sequences alignment. The scope of the paper focuses on speed optimization and memory reduction of the existing technique on initialization module. The novel development of the optimization using data compression technique for accelerates the Smith-Waterman (SW) algorithm has been revealed through this paper. This technique has been implemented on hardware based acceleration device. The development is targeted to Altera Cyclone II 2C70 FPGA and using 50 MHz oscillator. 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 tool. The theoretical analysis and simulation result based on implementation of the design using FPGA are presented and well organized in this paper. The comparative study based on theoretical and simulation results of this technique has been made to accomplish result of analysis. The compilation result for data compression technique development of SW algorithm consisting of 73 logic elements with 93.75% reduction in memory space requirement.