Research On Parallel Alignment Algorithm Of DNA Sequence Based On OpenCL Platform

The information age has arrived, the current computer environment is more complex and diverse, and so we need the potential of computer hardware. In computational science, there are heterogeneous system will just be able to become our best alternatives to do calculations and analysis. Open CL platform to build will achieve in heterogeneous environments GPU parallel algorithms. Currently, parallel alignment algorithm is also used in the field of bioinformatics, based on parallel algorithms will accelerate for the DNA sequence alignment to provide new ways. Therefore, Open CL parallel characteristics, focusing on the DNA sequence alignment related research.First, this paper introduces the relevant knowledge of Open CL base and DNA sequence alignment, and analyzes the role of Open CL on heterogeneous systems, describes the practical significance of bioinformatics DNA sequence alignment, and the DNA sequence alignment methods to study and summarize the developments at home and abroad.Secondly, we study the dynamic programming based on DNA sequence alignment algorithm, elaborated mathematical theory and rules for counting sequence alignment, the simulation Needleman-Wunsch algorithm and the Smith-Waterman algorithm based on dynamic programming algorithm of string on the JVC line design, the introduction of the "double penalty" mechanism, based on the Smith-Waterman algorithm for heterogeneous parallel design and implement a platform for Open CL heterogeneous parallel DNA sequence alignment algorithms, at last,the experimental data are given.Finally, this paper analyzes the platform for GPU Open CL optimization strategy for GPU architecture, this paper proposes a parallel strategy based on structural optimization GPU accelerated Smith-Waterman algorithm to achieve further optimization algorithm, and experimental results related to comparative analysis performance.