摘要
SNP位点选择是是国境口岸致病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。我们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,能够准确地寻找致病微生物的SNP位点组合,为大规模的检测基因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 the process of designing genechip probe for detecting pathogenic microorganism, the selection of single nucleotide polymorphism (SNP) combination is of great importance. At present, there is no automatic design method. This work is hard and the result is not always well. A new approach for selecting SNP combination is presented in this paper. Genetic algorithm is used to search optimal solution on the basis of classification ability of SNP combination, which is evaluated by the rough set theory. Other related experimental parameters are also incorporated. Experimental results show that the method can find out the best SNP combination pattern efficiently and accurately, thus demonstrating the reliability of this new method for designing the geneehip probe.
出处
《生物医学工程学杂志》
EI
CAS
CSCD
北大核心
2009年第3期643-646,652,共5页
Journal of Biomedical Engineering
基金
"十五"国家科技攻关计划项目"重大人兽共患病诊断平台"资助(2004BA519A44)