In this research we first propose to further develop the use of spatially defined arrays of oligonucleotide probes for sequence checking and de novo sequencing. Second, we will implement the technology in a pilot scale sequencing project. To accomplish this we will use the integrated chips, instrumentation, and software platform as defined in project 2 to explore: * Assays that discriminate perfect matches from mismatches. * Prediction of the hybridization intensities of probe-target combinations to aid in target specific array design. * Data analysis and sequence reconstruction algorithms using hybridization data. * The effectiveness of the assays in a pilot scale sequencing project. Successful completion of this work could lead to sequencing instrumentation that will provide order of magnitude improvements in DNA sequencing productivity.
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