Department of Network Systems, Toko University, Chiayi, Taiwan.
IEEE/ACM Trans Comput Biol Bioinform. 2012 May-Jun;9(3):837-45. doi: 10.1109/TCBB.2012.25.
Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphism (SNP). Designing a feasible primer pair is an important work before performing PCR-RFLP for SNP genotyping. However, in many cases, restriction enzymes to discriminate the target SNP resulting in the primer design is not applicable. A mutagenic primer is introduced to solve this problem. GA-based Mismatch PCR-RFLP Primers Design (GAMPD) provides a method that uses a genetic algorithm to search for optimal mutagenic primers and available restriction enzymes from REBASE. In order to improve the efficiency of the proposed method, a mutagenic matrix is employed to judge whether a hypothetical mutagenic primer can discriminate the target SNP by digestion with available restriction enzymes. The available restriction enzymes for the target SNP are mined by the updated core of SNP-RFLPing. GAMPD has been used to simulate the SNPs in the human SLC6A4 gene under different parameter settings and compared with SNP Cutter for mismatch PCR-RFLP primer design. The in silico simulation of the proposed GAMPD program showed that it designs mismatch PCR-RFLP primers. The GAMPD program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/gampd/.
聚合酶链反应-限制性片段长度多态性（PCR-RFLP）在与单核苷酸多态性（SNP）相关的复杂遗传疾病的小规模基础研究中非常有用。在进行 SNP 基因分型的 PCR-RFLP 之前，设计可行的引物对是一项重要的工作。然而，在许多情况下，用于区分目标 SNP 的限制酶导致引物设计不可行。引入诱变引物可以解决这个问题。基于 GA 的错配 PCR-RFLP 引物设计（GAMPD）提供了一种方法，该方法使用遗传算法从 REBASE 中搜索最佳诱变引物和可用的限制酶。为了提高所提出方法的效率，使用诱变矩阵来判断假设的诱变引物是否可以通过用可用的限制酶消化来区分目标 SNP。通过更新的 SNP-RFLPing 核心来挖掘目标 SNP 的可用限制酶。GAMPD 已用于在不同参数设置下模拟人类 SLC6A4 基因中的 SNP，并与用于错配 PCR-RFLP 引物设计的 SNP Cutter 进行比较。拟议的 GAMPD 程序的计算机模拟表明，它设计了错配 PCR-RFLP 引物。GAMPD 程序是用 JAVA 实现的，可以在 http://bio.kuas.edu.tw/gampd/ 免费获得。
