基因組是DNA中可以表現的片段，一段可以表現的基因是由很多基因組穿插著introns所組成。DNA經過轉錄和轉譯成蛋白質的過程中，會把introns切除，留下可以表現的基因組。許多研究者為了針對基因組做更深入的研究而需要設計可以在genome上包夾基因組片段的多對引子，再利用聚合

Exons are expression DNA sequences. A DNA sequence which includes gene has exons and introns. During transcription and translation, introns will be removed, and exons will remain to become protein. Many researchers need exon primers for PCR experiments. However, it is a difficult to find that many exon primers satisfy all primer design constraints at the same time. Here, we proposed an efficient exon primer design algorithm. The algorithm applies multiobjective genetic algorithm (MGA) instead of the single objective algorithm which can easily lend to unsuitable solutions. And a hash-index algorithm is applied to make specificity checking in a reasonable time. The algorithm has tested by a variety of mRNA sequences. These dry dock experiments show that our proposed algorithm can find primers which satisfy all exon primer design constraints.

1. Introduction 1
2. Background Materials and Literature Review 4
2.1. Background materials 4
2.1.1. PCR experiment and applications of PCR 4
2.1.2. Exon and Intron 5
2.1.3. Genetic Algorithm and Multiobjective Genetic Algorithm 6
2.2. Literature reviews 9
3. The constraints on PCR and exon primer design 13
3.1. Definition of the proposed algorithm 13
3.2. PCR constraints 14
3.3. Exon primer design 18
3.4. Specificity 20
4. The proposed algorithm 21
4.1. Problem Statement 21
4.2. Alignment 24
4.3. Initialization 24
4.4. Evaluation 25
4.5. Selection 26
4.6. Crossover 28
4.7. Mutation 29
4.8. The Hash-index Method for Specificity Checking 30
5. Dry dock experiments 34
6. Discussion 38
7. Conclusions 41
References 42

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