Current moIecuIar bioIogy techniques were deveIoped primarily for characterization of single genes, not entire genomes, and, as such, are not ideally suited to high resolution analysis of complex traits and the moiecular genetics of very large populations.Despite rapid progress in the human genome project effort, there is little doubt that radicaIIy new conceptual approaches are needed before routine whole genome-based analyses can be undertaken by both basic research and clinical laboratories.Physical mapping of genomes, using restriction endonucleases, has played a major role in the identification and characterizing various loci, for example, by aiding clone contig formation and by characterizing genetic lesions.Restriction maps provide precise genomic distances, unlike ordered sequencebased landmarks such as Sequence Tagged Sites (ST%), that are essential for optimizing the efficiency of sequencing efforts, and for determining the spatial relationships of specific loci.When compared to tedious hybridization-based fingerprinting approaches, ordered restriction maps offer relatively unambiguous clone characterization that is useful in contig formation, establishment of minimal tiling paths for sequencing, and preliminary characterization of sequence lesions.In addition, such maps provide a useful scaffold for sequence assembly, often critical in the final sequence finishing stage.Despite the broad applications of restriction maps, the associated techniques for their generation have changed little over the last ten years, primarily because they still utilize electrophoretic analysis.To help overcome these shortcomings, our laboratory developed the first practical non-electrophoretic genomic mapping approach, Optical Mapping, to meet this need.Optical Mapping is a single molecule methodology for the rapid production of ordered restriction