高成炎臺灣大學：資訊工程學研究所張嘉宏Chang, Chia-HungChia-HungChang2007-11-262018-07-052007-11-262018-07-052004http://ntur.lib.ntu.edu.tw//handle/246246/53762變異性重覆序列DNA（VNTR）是由一段一段相似、相鄰的序列所組成，大量存在於生物體內的去氧核糖核酸(DNA)中。由於他的長度多型性及特殊的遺傳特性，使得它被廣泛的應用在DNA 指紋圖譜技術、親緣辨識、以及疾病的分析上。在以往的實驗方式中，生物學家花費大量的時間跟金錢作生物實驗以在DNA中求得可能的變異性重覆序列位置。為了減輕生物學家的負擔，我們設計了一個程式--VNTR analyzer；這個程式會計算序列上的重複序列數目，並藉由比較不同亞種間相對應的重複序列數目，來預測、判斷可能的變異性重覆序列位置。我們並提供一個視覺化的工具，對可能的VNTR進一步的分析、判斷。最後，我們用Staphylococcus aureus, Xylella fastidiosa and Salmonella enterica這三個菌種來進行測試，發現大部分已知的VNTR區域都可被我們的程式成尼鋮魽F除此之外，我們還找到大量極富淺力的VNTR區域，可以拿來做進一步的實驗與研究。Variable number of tandem repeats (VNTR) stands for a tandem repeat which has variation in length and the number of repeated segments between individuals. VNTRs are useful as molecule markers in many applications, such as DNA fingerprinting, genetic disease analysis and molecular typing of prokaryotes. It costs a large amount of money and time to identify these special loci by using traditional biological experiments. Here we develop a novel tool, VNTR analyzer, to identify and analyze VNTR in genome sequence by comparing genomic sequences of different strains. In this study, we demonstrate its ability to detect VNTRs by analyzing 3 bacterial species: Staphylococcus aureus, Xylella fastidiosa and Salmonella enterica. The results showed that our program could find VNTRs accurately in a short time. Moreover, the program provides biologists a colorful visualization tool for further analysis.1 Introduction………………………………………………................1 2 SYSTEM AND METHOD……………………………………...…..4 2.1 Step 1. Searching for all possible tandem repeats………………6 2.2 Step 2. Locating corresponding loci in different strains………7 2.3 Step 3. Computing the variation of copies of tandem repeats in all strains………………………………………………………9 2.4 Step 4. Visualization tool for VNTR candidate……………….11 3 RESULT AND DISCUSSION…………………………...….…….14 3.1 Staphylococcus aureus………………………………………...16 3.2 Xylella fastidiosa…………………………………………….19 3.3 Salmonella enterica……………………………………………20 4 CONCLUSION…………………………………………………….21 附錄 A VNTR 形成機制及其重要性………………………………………….23 A.1 VNTR的形成機制………………………………………………23 A.2 用PCR實驗同時分析多個VNTR位置………………………...24 A.3 VNTR的應用……………...………………………………….....25 A.3.1 刑事鑑定..…………………………………..…………25 A.3.2傳染病的散播…………………………………….…….27 A.3.3親緣辨識………………………………………………..28 A.3.4疾病的分析………………………………...………...…29 B 視覺化工具的需要性及運作……………………………………….30 B.1計算重複序列數目的演算法………………………………….30 B.1.1使用區域性序列比對演算法…………………………..30 B.1.2 WDP演算法……………………….……………………..31 B.2 VNTR的判斷方法………………………………………………32 B.3 重複序列數目的不確定性………………………...…………33 B.4 程式參數的影響…………………………………………...…36 B.5 Gap penalty………………………………………………...…37 References………………………………………………………………392038042 bytesapplication/pdfen-US變異性重複序列預測Tandem repeatVNTR analyzerpredictVNTRVariable Number of Tandem Repeatthesishttp://ntur.lib.ntu.edu.tw/bitstream/246246/53762/1/ntu-93-R91922056-1.pdf