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Robotic "ridding" techniques, combined with novel molecular fixation techniques permit the biochemical action and evaluation of a large number of samples in parallel. Given the ability to grid multiple samples, and assay biochemistries on the single molecule level, we have developed an integrated system to robotically deposit samples, and image substrate molecules using automated fluorescence microscopy. To complement these automation advancements, we have developed new approaches for ordered restriction map construction using Bayesian inference techniques. These map construction algorithms work with maps automatically derived from single molecules, and are notably, the first practical approaches for the automated analysis of data derived from large populations of single molecules. Considered together, these advances constitute an integrated mapping system which eliminates operator interaction with the system from molecular deposition through map construction. The full utility of this system is derived ranging from the synthesis of new single molecule fixation effects, biochemistries and statistical analysis approaches, and should prove to be universally applicable to the analysis other single molecule systems.
High resolution mapping has enormous utility in the genomic analysis of mammalian genomes and microorganisms. Optical mapping is currently playing a major role in the international effort to sequence human genome by providing rigorous scaffolds for the assembly and verification of large scale sequencing efforts. Other applications in the laboratory are centered on the direct mapping of genomic DNA extracted from bacteria and pathogenic parasites-bypassing the need for libraries, with the goal of analyzing large number of strains to develop new approaches to the functional analysis of genomes.