Reconstruction of DNA Sequence Information from a Simulated DNA Chip Using Evolutionary Programming

DNA sequencing methods are the subject of continued interest in molecular biology for use in a wide variety of applications. Sequencing DNA by hybridization on a “DNA chip” has been estimated to increase the rate of DNA sequencing as much as one-million fold. In this process, the sequence of a target molecule is reconstructed by the complementary binding of a pool of random probe molecules. For each target, an appropriate probe length must be used to unambiguously determine the sequence of a given target sequence of length N. Using evolutionary programming, we have simulated the binding of probes of length four nucleotides to a series of target lengths to determine most optimal target length that can be unambiguously reconstructed. Evolutionary programming is demonstrated to be well suited to sequence reconstruction problems and could also be extended for gene expression monitoring with DNA chip technology.