MethPrimer: designing primers for methylation PCRs

被引：2255

作者：

Li, LC

Dahiya, R ^{[1
]}

机构：

[1] Vet Affairs Med Ctr, Dept Urol, San Francisco, CA 94121 USA

[2] Univ Calif San Francisco, San Francisco, CA 94121 USA

来源：

BIOINFORMATICS | 2002年 / 18卷 / 11期

关键词：

D O I：

10.1093/bioinformatics/18.11.1427

中图分类号：

Q5 [生物化学];

学科分类号：

071010 [生物化学与分子生物学]; 081704 [应用化学];

摘要：

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.

引用

页码：1427 / 1431

页数：5

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