What do the colors in the CpG track represent?

The CpG track displays CpGs in 4 colors: red, blue, green, and black. The color coding depends on which enzyme group the CpG dinucleotide belongs to:

  • methylation-sensitive restriction enzymes: AciI, HhaI, HpaII, HpyCH4V and BstUI (RE) - red,
  • methylation-dependent enzyme (McrBC) - blue,
  • both RE and McrBC - green,
  • other - black.
The Methyl-MAPS method is an enzyme-based approach using methylation-sensitive and -dependent enzymes to digest genomic DNA. Such color coding helps one identify potential recognition sites.