到現在為止，基因定序的研究主要在基因序列的組合，對於序列中的四種鹼基G,A,T,C如何判定及評估判定的品質雖有論及，但不多見。由於精準的鹼基判定在之後的序列組合，多樣性的偵測以及下游的分析上扮演著非常重要的角色，因此一個能降低錯誤預測率且能提供高品質的鹼基判定方法便顯得非常重要。本論文提出一新的對談矩陣估計方法，並以此來進行鹼基判定，另外，亦提出一簡單易懂且利用統計分配概念的品質指標，以評估利用新舊方法判定鹼基品質上之差異。

One important aspect of the Human Genome Research is to develop technologies for automated high-speed high throughput DNA sequences. A lot of efforts has been devoted to the assembly of the DNA sequence, very few of them, however, focuses on the prediction of the bases, not to mention the quality of the sequence call. As accurate base-calling plays a crucial role for assembly, polymorphism detection, and downstream analysis, a base-calling algorithm that is able to reduce the error rate in prediction, and hence upgrade the calling quality is a necessity. In this thesis, we develop an approach in estimating the cross-talk matrix for base-calling. Also, we combine the major features of the bases and develop an effective quality index in measuring the quality of the sequence call.

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