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iii CHAPTER 1 GENERAL INTRODUCTION 1 BIOLOGY OF AC/DS TRANSPOSON 1 DNA STRUCTURAL PROPERTIES 1 THESIS ORGANIZATION 2 REFERENCES 3 CHAPTER 2. DNAFVP: A PACKAGE FOR DNA FEATURE CALCULATION, VISUALIZATION AND VECTOR PREPARATION 5 ABSTRACT 5 INTRODUCTION 6 IMPLEMENTATION 7 DISCUSSION 15 ACKNOWLEDGEMENTS 15 REFERENCES 15 FIGURES 18 SUPPLEMENTARY INFORMATION 20 CHAPTER 3. COMPUTATIONAL PREDICTION OF DS TRANSPOSON INSERTION SITES IN PLANTS USING DNA STRUCTURAL FEATURES  48 ABSTRACT 48 INTRODUCTION 49 METHODS 50 RESULTS AND DISCUSSION 54 ACKNOWLEDGEMENTS 60 REFERENCES 60 TABLES 62 FIGURES 66 SUPPLEMENTARY INFOMATION 68 CHAPTER 4 GENERAL CONCLUSION 79 REFERENCES 80 ACKNOWLEDGEMENTS 83

Computational prediction of Ds transposon insertion sites in plants using DNA structural features