国境口岸食源性微生物检测基因芯片探针设计新方法的研究

New Method of Gene Chip Probe Design for Food-borne Microorganism Detection at Frontier Port

SNP位点选择是国境口岸食源性微生物基因芯片检测探针设计的关键环节,目前主要依靠手工完成,严重影响着检测速度和检测质量,为此提出了一种基于遗传算法的SNP位点的自动选择方法。该方法运用粗糙集理论评估SNP位点组合的分类能力,综合与检测实验密切相关的设计指标,采用遗传算法进行优化搜索。实验结果表明,该方法具有很好的稳健性和较快的收敛速度,能够准确地寻找食源性微生物的SNP位点组合,为大规模的检测芯片探针自动设计提供了快速可靠的途径,缩短了国境口岸致病微生物的检测时限,提高了检测结果的准确性。

In process of gene chip probe design for food-borne microorganism detection, the selection of SNP combination is of great importance. At present, no automatic design affected seriously speed and quality of defection. A new approach of select SNP combination is presented in this paper. Genetic algorithm is used to search optimal solution on the basis of classifying ability of SNP combination, which is evaluated by the rough set theory. Other correlative experimental parameters are also been incorporated. Experiment results showed that the method can find the best SNP combination pattern efficiently and accurately, which imply that it can be a reliable approach for the gene chip probe design .