A method and system for quickly comparing gene data

Abstract

The embodiment of the invention discloses a method for quickly comparing gene data, which comprises the following steps: an FPGA reads genes to be compared and a reference gene from a buffer, and thelength of the genes to be compared is L; the FPGA determines a plurality of target seeds from a reference gene accord to a gene to be aligned and a preset algorithm, and the target seeds are gene sequences match with the gene to be aligned for a certain length; the FPGA selects the seeds with the highest similarity from multiple target seeds as the optimal seeds; according to the position of the best seed in the reference sequence, the FPGA obtains the gene sequence with preset length, and the length of the gene sequence is greater than or equal to the length of the best seed; the FPGA scoresthe best seeds by calculating the shortest editing distance between the best seeds and the estimated sequence, and the score is used to indicate the accuracy and authenticity of the best seeds; the FPGA outputs an optimal comparison result according to the scoring of the optimal seeds. The throughput performance of the algorithm can be improved and the efficiency of gene alignment can be improved.

Description

technical field [0001] The present application relates to the field of gene analysis, in particular to a method and system for quickly comparing genetic data. Background technique [0002] The study of genes also has a profound impact on the major progress of human beings. The comparison of gene data is also the basic composition and important foundation of bioinformatics. The basic method of gene comparison is to arrange two or more sequences together to indicate their similarity. place. Intervals can be inserted in the sequence, and corresponding identical or similar symbols are arranged on the same column. The base pair can be regarded as the basic unit of DNA. A base pair is a pair of bases that match each other and are connected by hydrogen bonds according to certain matching rules. The bases that make up a base pair include A adenine, T Thymine, C cytosine, G guanine, the matching rules are A—T, G—C. [0003] Genetic data comparison is one of the longest time-consum...

AI Technical Summary

Problems solved by technology

[0004] However, this algorithm is designed for the purpose of saving memory, and the algorithm structure is relatively complicated. It mainly compares genes through a serial method, which leads to excessive resource consumption, long time consumption and low comparison efficiency. The performance bottleneck of the entire genetic data analysis process

Images