Simulation sutudy for high-speed DNA sequencing

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An unknown DNA sequence is called a target DNA.A panel on which all possible sequences of oligonucleotide probes (ONPs) of a certain length are arranged in mesh-like form is called an oligonucleotide-panel and each ONP is called a DNA probe. Computer handling method based on hybridization information between the target DNA and DNA probes is called a sequencing by hybridization method (SBH in abbreviation) hereafter. Applicability of a genetic algorithm to the SBH method has been prved by this studies under the following condetions. Condetion 1) There is no mismatch between the DNA probes and the target DNA.Condition 2) Multiple hybridizations of certain probes to the target DNA are allowed. Conditon 3) The target DNA is not separated into two fragments.Computer simulation of the algorithm for DNA sequencing reveals the following facts. 1) Longer bases in ONP is more useful, but too much longer bases requires much longer computation time. 2) The method can be applied to more than 10K-bases segment of DNA.Improvement of the algorithm for handling mismatch-free hybridezations will be a future problem.