Optical mapping experiment. In an optical mapping experiment, stretched DNA molecules are deposited on a charged glass surface using an array of microfluidic channels (a) and digested with a methylation-insensitive restriction enzyme that cuts the DNA at specific sequence based recognition sites (b). The stretched DNA relaxes around the cut sites, but in the process, small restriction fragments can be lost through desorption. The DNA molecules are then stained with fluorescent dye and imaged. Restriction fragments are identified with machine vision and the fragment lengths are estimated by integrating fluorescent intensity (c). For each molecule this produces an ordered listing of restriction fragment lengths known as an Rmap (d).