Implementation Of Myers Algorithm For Gene Sequence Alignment On FPGA

From the end of the last century to the beginning of the 21 th century,with the in-depth implementation of the human genome project and various types of genetic engineering,bioinformatics data is increasing at an exponential rate.This biological information will affect research and development in pharmacy,medicine,agriculture,and environmental protection,and will likely help people improve their quality of life.One of its main technologies for civilian use is gene sequencing.Gene sequencing,as a new type of gene detection technology,can extract the full sequence of genes from blood and even saliva,and determine the full sequence of genes,so as to analyze the possibility of disease in the gene data,and then provide scientific guidance.So that the treatment is correct.In terms of application value,the speed of gene sequencing is accelerated,and diseases can be identified faster,so that sufficient time can be obtained for the treatment stage,not only improve the cure rate of cancer,but also reduce birth defects,and improve human health.In the dissertation,through analyzing the calculation principles and speed of each sequence alignment,the Myers algorithm is proposed as a global sequence alignment algorithm in gene sequencing,and it is implemented on FPGA to accelerate the speed of gene sequencing.By analyzing the PE module circuit implemented by the Myers algorithm,the key circuits are optimized to reduce the delay,so that the clock frequency of the entire system can be improved to increase the calculation amount of the system.Experimental results show that the clock frequency of the system running on the KCU1500 board can reach 181 MHz,and it can process 70.32 million pairs of gene sequences per second,which is 56 times that running on the CPU.The main research contents and completed work of the dissertation include:1)Understand the research status of the alignment of various gene sequences,and analyze that Myers algorithm is faster than Needleman-Wunsch algorithm in principle and structure.At the same time,analyze the advantages and disadvantages of Myers algorithm implementation on different platforms.2)The Myers algorithm is implemented in a pipelined and parallel manner on FPGA to achieve faster speed.At the same time,it is analyzed that several circuit paths in the PE module circuit are relatively long,affecting the clock frequency of the entire system.These circuits are reasonably optimized using registers to divide the circuit into four parts,thereby reducing circuit delay and increasing clock frequency.3)The number of different PE modules will affect the performance of the system.By analyzing the test data,the appropriate number of PE modules is selected,which makes the system use less resources and higher throughput.