有許多的方法已經應用在RNA二級結構的預測上，而一般用的dynamic programming的方法，只能預測較短的序列，對於較長的序列效果不佳。RAGA是一個基因演算法，可以預測較長序列的結構預測，藉由已知的兩條RNA序列以及其中一條序列的結構，可以用來預測另一條序列的結構。為了改善RAGA的效能，在這裡我們增加了一條運算式在基因演算法裡，使得兩條序列在重新對齊時能得到較好的結果，接著我們比較幾種不同預測RNA二級結構的方法，包括RAGA，發現RAGA結合了我們的方法能夠得到比較好的結果。

Many methods can be used to predict the secondary structure of an RNA sequence. One of the methods is the dynamic programming approach. However, the dynamic programming approach takes too much time. Thus, it is not practical to solve the problem of long sequences with dynamic programming. RAGA (RNA Sequence Alignment by the Genetic Algorithm) is a genetic algorithm to align two similar sequences that the structure of one of them (master sequence) is known and another (slave sequence) is unknown. We can predict an RNA sequence by analyzing several homologous sequence alignment. In this thesis, we add an operator to mutate the residues of the base pairs in the master sequence and realign two sequences again. We compare our operator with other traditional operators, such as crossover and mutation. The experiment results show that our new operator gets a big improvement.

TABLE OF CONTENTS
Page
LIST OF FIGURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
LIST OF TABLES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0
Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Chapter 2. Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1 Evolution Through Natural Selection - The Fitness Survives . . . . . 5
2.2 Genetic Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Chapter 3. RNA Sequence Alignment by the Genetic Algorithm . . 7
3.1 Objective Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3.2 GA operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.3 The Procedure of RAGA . . . . . . . . . . . . . . . . . . . . . . . . . 12
Chapter 4. Our Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Chapter 5. Experiment Results . . . . . . . . . . . . . . . . . . . . . . . 22
Chapter 6. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
BIBLIOGRAPHY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

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