A gene structure predicting method and program for accurately predicting an unknown gene region and its structure from a genome base sequence on the basis of tiling array data. Using a tiling array where partial base sequences regularly extracted from a genome base sequence are arranged as probes, tiling array data on the manifestation intensity of each probe measured by using the tiling array and genome base sequence data on the genome base sequence are acquired. On the basis of the acquired tiling array data, the manifestation region of a gene in the genome base sequence is estimated. Starting from the base corresponding to the estimated manifestation region, the attributes about the gene structure of the bases adjacent to the starting base are determined on the basis of the tiling array data and the genome base sequence data are predicted.
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