近年來由於核糖核酸病毒的變異速率快，常演化出不同的病毒株，造成人們初次遇到時常措手不及造成大規模的流行甚至死亡，如禽流感。因此針對核糖核酸病毒來探索其序列、功能與演化的關係是目前一個相當重要的研究課題。在這篇論文中我們藉由序列比對工具的技術針對流感病毒甲型的十一段蛋白質序列做分析。研究對象主要有兩個1.流感病毒上的重要功能位置2.流感病毒上物種限制的位置。針對功能位點我們收集人類史上嚴重的1918年西班牙流感、2009年新流感去做分析。針對物種限制位點我們收集人、鳥禽類、豬三群去分析。最後我們將功能及物種限制位點作交互比對，希望能找出真正屬於功能以及物種限制的位點。

In recent years, since the mutation rate of RNA virus is faster than that of DNA virus, it induces that there are many new viruses evolved from the evolution. These viruses may cause calamities at various countries and seasons, such as the avian influenza H5N1. It is an important topic to analyze the relationships among sequences, function, and evolution of RNA virus. In this thesis, we used multiple sequence alignment tools to analyze eleven protein segments of influenza A virus. Our research had two major goals, one is to find important function sites for influenza A virus, and the other one is to find species-associated sites for influenza A virus. Thus, we collected the 1918 Spanish influenza virus which was the devastating pandemic disease in the history and the pandemic disease 2009 to analyze for important function sites. We divided human, avian, and swine into three groups to find species-associated sites. Finally, we wanted to distinguish function and species-associated sites, and find the real meaning of each position in the sequence for influenza A virus.

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