Shotgun DNA mapping involves three steps: 1) digesting genomic DNA into fragments, 2) unzipping the fragments and recording the force curves, and 3) comparing the experimental force curves to a library of simulated curves to match fragments to locations in the genome. The document discusses how unzipping DNA can detect proteins bound to it based on deviations in the force curve from naked DNA. It presents results matching an experimental plasmid unzipping force curve only to the corresponding simulated plasmid curve within a library simulating an entire yeast genome.