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Associate PCR-RFLP Assay Design With SNPs Based on Genetic Algorithm in Appropriate Parameters Estimation

机译:基于遗传算法的SNP关联PCR-RFLP检测设计参数估计

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Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is a commonly used laboratory technique and useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphisms (SNPs). Before PCR-RFLP assay for SNP genotyping can be performed, a feasible primer pair observes numerous constraints and an available restriction enzyme for discriminating a target SNP, are required. The computation of feasible PCR-RFLP primers and find available restriction enzymes simultaneously aim at a target SNP is a challenging problem. Here, we propose an available method which combines the updated core of SNP-RFLPing with a genetic algorithm to reliably mine available restriction enzymes and search for feasible PCR-RFLP primers. We have in silico simulated the method in the SLC6A4 gene under different parameter settings and provided an appropriate parameter setting. The wet laboratory validation showed that it indeed usable in providing the available restriction enzymes and designing feasible primers that fit the common primer constraints. We have provided an easy and kindly interface to assist the researchers designing their PCR-RFLP assay for SNP genotyping. The program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/ganpd/.
机译:聚合酶链反应限制片段长度多态性(PCR-RFLP)是一种常用的实验室技术,可用于与单核苷酸多态性(SNP)相关的复杂遗传疾病的小型基础研究。在可以进行SNP基因分型的PCR-RFLP分析之前,可行的引物对必须遵守许多限制条件,并且需要一种可用于识别目标SNP的限制酶。计算可行的PCR-RFLP引物并同时找到可用于目标SNP的限制性酶是一个具有挑战性的问题。在这里,我们提出了一种可用的方法,该方法将SNP-RFLPing的更新核心与遗传算法相结合,以可靠地挖掘可用的限制酶并搜索可行的PCR-RFLP引物。我们已经在计算机上模拟了SLC6A4基因在不同参数设置下的方法,并提供了适当的参数设置。湿实验室验证表明,它确实可用于提供可用的限制酶和设计适合常见引物限制条件的可行引物。我们提供了一个简单友好的界面来协助研究人员设计用于SNP基因分型的PCR-RFLP分析。该程序在JAVA中实现,可从http://bio.kuas.edu.tw/ganpd/免费获得。

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