Improvement Of Smith Waterman Gene Sequencing Algorithm And Research On Hardware Acceleration Method

Since the beginning of this century,with the rapid development of gene sequencing technology,the cost of gene sequencing for individuals has dropped significantly,resulting in a rapid increase in the amount of gene sequencing data,making the current speed of analysis of gene data no longer The speeds match,and there is a mismatch,so this paper improves the Smith Waterman algorithm commonly used in gene sequencing and studies hardware acceleration.This article starts with the research background and significance of the algorithm,and outlines the basic principles of gene sequencing.Through an indepth analysis of the Smith Waterman algorithm,it is optimized and improved:First,based on the characteristics of the initialization matrix of the algorithm,it is improved from the principle of the algorithm,reducing the scoring step of the two-dimensional dynamic matrix,thereby reducing the complexity of the algorithm Degree;secondly,using the feature of the algorithm that there is no dependency between the elements on the diagonal of the two-dimensional dynamic matrix,combined with the idea of the pulsating array,so that the algorithm can be parallelized on hardware;then through the block of the matrix And delete strategy to optimize the hardware system and reduce the amount of calculation of the hardware system,so as to achieve the parallel improvement of the algorithm;finally designed an FPGA sequencing platform that meets the requirements of parallelization.By simulating the Smith Waterman algorithm before and after the improvement,the results prove that the improved algorithm has significantly shorter sequencing time for gene sequences of the same size,which improves the efficiency of operation.Therefore,the algorithm improvement scheme of thispaper is feasible.