Parallel processing cell score design of linear gap penalty smith-waterman algorithm

In this paper, the optimize computational processing element for linear smith-waterman algorithm cell score based on the parallel computational approach is introduced. Two bits optimized comparator block were used to compare the DNA sequence characters, while the computation block was used to complete computation towards reducing the numbers of components involved. The complete architecture is designed and developed in Altera Quartus II version 13.0 and targeted to Altera Cyclone IV EP4CE115 Field Programmable Gate Array (FPGA). In realizing the important of the logic functionality of the design, the modular design approach has been adapted to this design. The simulation over the module and complete architecture were used for validating the design against the expected result. Finally, the result obtained from the study indicates that the optimized computational processing element design for linear smith-waterman algorithm cell score based on the parallel computational approach is feasible to be implemented in the DNA sequence alignment as the processing element.