Simulation sutudy for high-speed DNA sequencing

一个未知的DNA序列被称为靶DNA，一个面板上的所有可能的序列的寡核苷酸探针（ONP）的一定长度排列成网状的形式被称为一个寡核苷酸面板，每个ONP被称为一个DNA探针。基于靶DNA和DNA探针之间的杂交信息的计算机处理方法在下文中被称为杂交测序法（缩写为SBH）。在以下条件下，遗传算法对SBH方法的适用性已被证明。条件1）DNA探针与靶DNA之间不存在错配。条件2）允许某些探针与靶DNA进行多次杂交。条件3）目标DNA没有被分离成两个片段。DNA测序算法的计算机模拟揭示了以下事实。1)在ONP中，更长的基更有用，但是太长的基需要更长的计算时间。2)该方法适用于10K碱基以上的DNA片段，进一步改进算法以处理无错配杂交是今后的研究方向。

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.