| ABSTRACT | 第1-10页 |
| 摘要 | 第10-17页 |
| Introduction | 第17-37页 |
| 1 Codon usage bias | 第17-23页 |
| ·The phenomenon of codon usage bias | 第17-18页 |
| ·Hypotheses for codon usage bias | 第18-19页 |
| ·Codon usage, translation and gene function | 第19-23页 |
| 2 Codon pair usage | 第23-29页 |
| ·Codon pair bias | 第23页 |
| ·Codon pair bias and translation | 第23-29页 |
| 3 Translation efficiency | 第29-32页 |
| ·Different definitions of translation efficiency in the literature | 第29-30页 |
| ·Measuring TE by computational method | 第30-32页 |
| 4 Common measures of codon bias and codon pair bias | 第32-37页 |
| ·Relative synonymous codon usage (RSCU) | 第32页 |
| ·Effective number of codons and ENC | 第32页 |
| ·Codon adaptation index and eCAI | 第32-33页 |
| ·Correspondence analysis on codon usage | 第33页 |
| ·tRNA-adaptation index | 第33-35页 |
| ·Codon pair score and Codon pair bias | 第35-37页 |
| Experimental study | 第37-93页 |
| 5 Analysis of codon pair bias in 478 organisms | 第37-71页 |
| ·Genome wide codon pair bias in 478 organisms | 第37-65页 |
| ·Materials and Methods | 第37-47页 |
| ·Datasets | 第37页 |
| ·Codon pair score and codon pair bias | 第37-40页 |
| ·Program source codes | 第40-47页 |
| ·Results | 第47-65页 |
| ·Codon pair bias of 9 model organisms | 第47-51页 |
| ·Codon pair bias is increased near the 5’end of CDSs | 第51-56页 |
| ·The length of the codon pair ramp | 第56-60页 |
| ·CPB for the first 40 codon pairs | 第60-63页 |
| ·Codon pair ramp in the last 120 codon pairs of all CDSs | 第63-65页 |
| ·Comparison between wild profiles and random profiles | 第65-71页 |
| ·Materials and Methods | 第65-68页 |
| ·Dataset | 第65页 |
| ·Randomization of averaged CPS profiles | 第65页 |
| ·R program source codes for Randomization | 第65-68页 |
| ·Results | 第68-71页 |
| 6 Analysis the correlation between CPB ramp and translation speed | 第71-93页 |
| ·Comparison between CPB ramp and translation speed for 478 species | 第71-90页 |
| ·Materials and Methods | 第71-80页 |
| ·Datasets | 第71页 |
| ·Measure of the translation speed for each codon pair | 第71-73页 |
| ·Java programs for calculating tAI of each CDS | 第73-78页 |
| ·Java programs for calculating tAI profile for a given genom | 第78-80页 |
| ·Results | 第80-90页 |
| ·The correlation between CPB and tAI of each CDS | 第80-85页 |
| ·The correlation between CPB and translation speed | 第85-90页 |
| ·The effect of codon pair usage on the translation of GFP genes | 第90-93页 |
| ·Materials and Methods | 第90-92页 |
| ·Datasets | 第90页 |
| ·Java program source code | 第90-92页 |
| ·Results | 第92-93页 |
| 7 Discussion | 第93-98页 |
| 8 Conclusions | 第98-99页 |
| 9 References | 第99-115页 |
| 10 Supplementary information | 第115-174页 |
| Abbreviations | 第174-176页 |
| Acknowledgements | 第176-177页 |
| Curriculum Vitae | 第177页 |
