摘要
分析A型流感病毒的八段蛋白質序列，能幫助我們更了解此病毒，但是隨著電腦科技不斷的進步，被定序出的A型流感病毒蛋白質序列也呈現等比級數的增加，要同時比對與分析如此大量的蛋白質序列，除了要不斷開發新的比對工具外，還需要替換更先進的硬體設備。本研究利用分散式運算的概念使用JAVA程式語言開發蛋白質序列分群分析軟體，將龐大的蛋白質序列拆解成數個檔案後再個別運算，因此縮短了比對蛋白質序列的執行時間，最後再藉由PRIMER 5程式，產生年代、國家和宿主的MDS相似度分析圖與UPGMA分析圖，由分析圖中發現1997年到2006年中，A型流感病毒的HA與NA蛋白質序列有著很高的相似性，在由國家的分析圖中，可以看出亞洲各國家的HA與NA蛋白質序列有明顯的相似性，不過亞洲各國家和中國的相似性不高，宿主中的分析圖中，野鳥、雞、鴨和豬的HA與NA蛋白質序列相似性很高，而豬是A型流感病毒發生跨物種傳染給人類的重要媒介，綜合以上結果顯示，A型流感病毒發生跨物種傳染給人類有一定的可能性。

Abstract
Analyzing the eight genomic protein segments of influenza A virus could provide a better understanding of this specific virus. Along with the progress of computer technology, numerous influenza A virus protein sequences were available in various internet data banks. However, analyzing a large number of protein sequences is a cumbersome work. Thus it is necessary to develop new tools with algorithmic method. This study used distributed method to develop a protein sequence clustering analysis software by JAVA programming language. The software could split a large number of protein sequences downloaded from NCBI into several files. Because of these individual files were calculated at the same time, therefore it could reduce the time in process of comparison and analysis. Finally, we used PRIMER 5 program to analyze these individual files and produce similarity analysis chart diagrams of MDS and UPGMA. In The similarity analysis chart diagrams indicated high homology in genomic protein segments of influenza A virus from year 1997 to 2006. The analysis also showed the genomic protein segments of influenza A virus are similar in Asia countries. However, the similarity between Asian countries and China is not significant. From analyzing the hosts, the genomic protein segments of influenza A virus are highly similar in species such like birds, chickens, ducks and pigs. Therefore, our data strongly support that the possibility of influenza A viruses can cross species to infect humans.

目 錄
致謝 Ⅰ
摘要 --------------------------------------------------------------------------- Ⅱ
Abstract ------------------------------------------------------------------------ Ⅲ
目錄 --------------------------------------------------------------------------- Ⅳ
表目錄 ------------------------------------------------------------------------ Ⅵ
圖目錄 ------------------------------------------------------------------------ Ⅶ
壹、前言 1
一、流行性感冒病毒(influenza virus) ------------------------------------------- 1
二、禽流感病毒(avian influenza virus) ------------------------------------------ 3
三、ClustalW多重序列比對(multiple sequence alignment)------------------ 3
四、JAVA程式----------------------------------------------------------------------- 4
五、分散式運算(distributed computing)----------------------------------------- 5
六、研究目的 ----------------------------------------------------------------------- 6
貳、材料與方法 7
一、實驗所使用的電腦環境------------------------------------------------------- 7
二、流感蛋白質序列來源---------------------------------------------------------- 7
三、多蛋白質序列比對軟體------------------------------------------------------- 7
四、親源樹狀圖軟體---------------------------------------------------------------- 8
五、影像處理軟體ImageJ --------------------------------------------------------- 9
六、分析資料的軟體PRIMER 5-------------------------------------------------- 10
七、JAVA程式語言----------------------------------------------------------------- 11
八、蛋白質分群分析流程---------------------------------------------------------- 12
九、蛋白質序列分群分析軟體(Protein Clustering Analysis software)------ 14
十、下載A型流感病毒蛋白質序列--------------------------------------------- 17
十一、使用蛋白質序列分群分析軟體------------------------------------------- 18
十二、本研究實驗範圍------------------------------------------------------------- 28
參、結果 30
一、年代MDS相似圖結果-------------------------------------------------------- 33
二、年代加入Factory因子的MDS相似圖結果------------------------------ 34
三、年代的UPGMA分析圖結果------------------------------------------------- 35
四、國家MDS相似圖結果-------------------------------------------------------- 36
五、國家加入Factory因子的MDS相似圖結果------------------------------ 37
六、國家的UPGMA分析圖結果------------------------------------------------- 37
七、宿主MDS相似圖結果-------------------------------------------------------- 38
八、宿主加入Factory因子的MDS相似圖結果------------------------------ 39
九、宿主的UPGMA分析圖結果------------------------------------------------- 40
肆、結論 42
伍、參考文獻 47
陸、圖表 51
附錄A ------------------------------------------------------------------------- 87
附錄B ------------------------------------------------------------------------- 88
附錄C ------------------------------------------------------------------------- 89
附錄D ------------------------------------------------------------------------- 92
附錄E ------------------------------------------------------------------------- 93
附錄F ------------------------------------------------------------------------- 94

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