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      MethPrimer: designing primers for methylation PCRs

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      Bioinformatics
      Oxford University Press (OUP)

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          Abstract

          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. MethPrimer, based on Primer 3, 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.

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          Author and article information

          Journal
          Bioinformatics
          Bioinformatics
          Oxford University Press (OUP)
          1367-4803
          1460-2059
          November 01 2002
          November 01 2002
          : 18
          : 11
          : 1427-1431
          Article
          10.1093/bioinformatics/18.11.1427
          12424112
          43061fd0-1437-4541-afd4-4e2fba8e8bb1
          © 2002
          History

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