DNA 微陣列(Microarray)技術廣泛使用在分子生物學和 DNA 計算領域方面。在進行微陣列實驗之前，必須先得到一組探針(probe)，這些探針本身是與所感興趣的目標基因互補的DNA子字串；而且實驗的可靠性大大地與探針序列的品質有關。因此，我們必須小心謹慎地在目標序列選擇探針。對於探針設計策略，我們提出使用多目標基因演算法的新方法來解決。所提出的演算法能有效率的找出一組可用的探針，並且使用以後置樹(suffix tree)為基底的模組加速單一性(specificity)限制條件檢查。實驗結果顯示，我們所提出的演算法可對DNA微陣列同時設計出多個探針，這些探針不僅遵循設計特性，而且具有單一性。

DNA microarrays are widely used techniques in molecular biology and DNA computing area. Before performing the microarray experiment, a set of subsequences of DNA called probes which are complementary to the target genes of interest must be found. And its reliability seriously depends on the quality of the probe sequences. Therefore, one must carefully choose the probe set in target sequences. A new method for probe design strategy using multi-objective genetic algorithm is proposed. The proposed algorithm is able to find a set of suitable probes more efficient and uses a model based on suffix tree to speed up the specificity constraint checking. The dry dock experimental results show that the proposed algorithm finds several probes for DNA microarray that not only obey the design properties, but also have specificity.

Contents
Chapter 1. Introduction 1
Chpater 2. Background materials and literature reviews 4
2.1 Background materials 4
2.1.1 DNA microarray 4
2.1.2 Multi-objective Optimal Genetic Algorithm 5
2.2 Literature reviews 10
Chapter 3. Definition of the constraints on probe design 13
Chapter 4. The proposed algorithm 16
4.1 Encoding 18
4.2 Initialization 19
4.3 Fitness evaluation 19
4.3.1 Objectives of the problem 19
4.3.2 Mathematic model 27
4.4 GA Operator 28
4.4.1 Selection 28
4.4.2 Crossover 30
4.4.3 Mutation 33
Chpater 5. Experiments 38
5.1 Materials 38
5.2 Dry dock experiments 39
Chpater 6. Discussion 46
Chpater 7. Conclusions 47
References 48

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