MethPrimer: designing primers for methylation PCRs
MethPrimer: designing primers for methylation PCRs
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DOI：
10.1093/bioinformatics/18.11.1427
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发表时间：
2002-11-01
期刊：
影响因子：
5.8
通讯作者：
Dahiya, R
中科院分区：
文献类型：
--
作者：
Li, LC;Dahiya, R
动机：DNA甲基化是基因调控的一种表观遗传机制。基于亚硫酸氢盐转化的PCR方法，如亚硫酸氢盐测序PCR （BSP）和甲基化特异性PCR (MSP)，仍然是甲基化定位最常用的技术。现有的标准PCR引物设计程序无法处理基于亚硫酸氢盐转化的PCR引物设计，因为亚硫酸氢盐处理会导致DNA序列上下文的变化，而且对引物和该实验需要扩增的区域都有许多特殊的限制。因此，本研究旨在为此类应用开发一个程序。结果：MethPrimer是基于Primer3设计的用于甲基化定位的PCR引物设计程序。它首先以DNA序列作为输入，在序列中搜索潜在的CpG岛。然后在预测的CpG岛或用户指定的区域周围选择引物。MethPrimer可以设计BSP和MSP引物。读本选择结果通过网页浏览器以文本和图形形式呈现。
Motivation: DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP), remain the most commonly used techniques for methylation mapping. Existing primer design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based PCRs due to changes in DNA sequence context caused by bisulfite treatment and many special constraints both on the primers and the region to be amplified for such experiments. Therefore, the present study was designed to develop a program for such applications.Results: MethPrimer, based on Primer3, is a program for designing PCR primers for methylation mapping. It first takes a DNA sequence as its input and searches the sequence for potential CpG islands. Primers are then picked around the predicted CpG islands or around regions specified by users. MethPrimer can design primers for BSP and MSP. Results of primer selection are delivered through a web browser in text and in graphic view.