| Key Words | .... 2 | |
| Abstract | .... 2 | |
| 1 | Introduction | .... 3 |
| 2 | Why is an intelligent refiner necessary? | .... 5 |
| 2.1 | Computationally Optimal alignment | .... 5 |
| 2.2 | Biological reliability of computationally Optimal alignment | .... 7 |
| 2.3 | Possibility of Interferece of Biological Optimal alignment from computational ly Optimal alignment | .... 9 |
| 3 | Multiple Alignment System with Intelligent Refiner | .... 11 |
| 3.1 | Framework of the Alignment System with Intelligent Refiner | .... 11 |
| 3.2 | Intelligent Refiner | .... 12 |
| 4 | Example of Application | .... 21 |
| 5 | Disccusion | .... 23 |
| Acknowledgement | .... 25 | |
| References | .... 26 | |
| End | .... 27 |
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