多重序列比對是找出生物序列相互關系的一種知名方式，而結構區塊在蛋白質中是一種可進化的單位。基本上，包含相似結構區塊的蛋白質會被視為是同源的，因為結構區塊有這樣的特性，在做序列比對時，它們值得列入考量中。但是，大部份的多重序列比對工具都略過結構區塊這項資訊，在這篇論文中，我們提出一個基於結構區塊的多重序列比對工具──DOBALI。DOBALI會在執行多重序列比對之前做一些前處理，它讓使用者指定結構區塊的位置，接著，可能的結構區塊會被偵測出來，片段的結構區塊會被合併重組，之後，相同種類的結構區塊會以使用者選擇的現有的MSA工具來做序列比對。我們會在結果中展示出在某些情況下DOBALI會表現的比沒做前處理的時候還要好。

Multiple sequence alignment (MSA) is a method to find the relationship between biological sequences. A Domain is an evolutionary unit in protein. Generally, the proteins contains similar domains are seen as homologous. Because domains have such properties, they are worth of being taken into account when doing alignments. However, most MSA tools ignore the information about domains. In this paper, a domain-based multiple sequence alignments tool – DOBALI is introduced. DOBALI performs preprocesses before doing MSA. It lets users assign the positions of domains. Then, the possible domains are detected, and the segmented domains are combined and rearranged. After that, all the same kinds of domains are aligned together by an existing MSA tool chosen by the users. The result shows the alignments are better than which produced by none-preprocessing in some conditions.

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