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研究生:房俊傑
研究生(外文):Jun-Jeng Fen
論文名稱:建立人類Y染色體三核甘酸重複序列資料庫系統
論文名稱(外文):Establishment of Bioinformatic Database of Tri-nucleotide Repeats in Human Chromosome Y
指導教授:陳啟清陳啟清引用關係
指導教授(外文):Chen, Chi-Ching
學位類別:碩士
校院名稱:國立成功大學
系所名稱:生物學系碩博士班
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2002
畢業學年度:90
語文別:中文
論文頁數:46
中文關鍵詞:生物資訊微衛星Y染色體三核甘酸重複序列資料庫
外文關鍵詞:Y chromosomebioinformaticsdatabaserepeatTNRmicrosatellite
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Y染色體的有無決定了人類的性別。然而,人類成對染色體的比較中,性染色體是成對染色體中差異最為明顯。Y染色體與其它體染色體間有許多的差異:在Y染色體中,大部分的區域並沒有重組的現象;並且,在Y染色體中可以發現具有大量重複的DNA序列。Microsatellite DNA是一段短序列呈現序列重複現象的DNA片段,它們大多是高度的多型性,最近的許多學者,常利用Y染色體上的microsatellite作為親源鑑定或是族群演化的研究工具。
Data mining主要是用來研究如何在龐大的資料庫中整理並發現出隱藏的有用資訊。利用data mining對於資料庫的應用概念,利用程式針對microsatellite的特性,對於Ensembl database加以分析、整理,重新建立一個以microsatellite特性為主的資料庫系統,將是這次研究的主要目的之一。
在這次的研究中,我們新設計了一個專為microsatellite應用的模組,這個模組主要提供了兩個部分:一個是針對microsatellite所使用的重複序列由電腦自行排列組合,產生可能的重複序列單元;另一個部分則是提供了連結到遠端資料庫的方法,使得使用者不必再自行等待下載所需要分析的序列片段。當microsatellite database被建立後,利用關鍵索引欄位,可以快速的與其他資料庫進行模擬比對的工作。如此利用程式加以分析,不僅可以所花費的時間大幅減少,也免去了過去人工比對所可能產生的誤差。
很多的數據和資料僅僅只是以文字的方式加以表達,很難在極短的時間內找出可能的關聯性。因此,本次研究中加入了圖形的呈現,透過圖形的繪製,將有助於釐清並且集中焦點在可能的關聯性
Sex is determined by the presence or absence of the Y chromosome in humans. Of all human chromosomes, there are most difference in the X chromosome and Y chromosome. Y chromosome does not recombine during meiosis over most of its length and it is composed the high density of repeated sequence. Microsatellite is consisted short tandem repeat sequence. Microsatellite is abundant and polymorphic in common eukaryotic genome, so it has been used as genetic markers to molecular biology studies as useful tools in gene mapping, population genetics, etc.
Data mining is the object that it can assist to find the hidden useful information in the great database. One of the researches, we take advantage of data mining to coding some programs for building the microsatellite database system.
In the researches, we coded the Perl programs module specific to microsatellite analysis. This module provides several outstanding advantages in definition and searching for microsatellite investigation. First, every possible and suitable repeat patterns could be generated and output automatically by random arrangement and combination via computer science. Second, local users could find desirous DNA sequence for repeats analysis directly by connecting to remote DNA database instead of download any DNA sequence. Finally, when microsatellite database had ever been constructed, researcher could embed other databases, such as disease or SNP databases, for further research rapidly by key word index fields. This study provide a powerful methods, which not only saving considerable time and harddisk loading for but avoiding possible artificial error of analysis process in repeat sequence investigation.
The data display not only by words but by figures will contribute to appear the relation of microsatellite in human Y chromosome. We preferred to the application of the figures in the microsatellite analysis researches.
英文摘要
中文摘要
誌謝
圖目錄 …………………………………………………………………1
表目錄 …………………………………………………………………2

第一章 前言
一、 Y chromosome ……………………………………………3
二、 Microsatellite ………………………………………………3
三、 Bioinformatics ……………………………………………4
四、 Relational database ………………………………………4
五、 Ensembl database …………………………………………5
六、 Data mining and microsatellite database …………………6
七、 Data merge …………………………………………………7
八、 Program Coding Perl and Bioperl and Figure Expression (GD Library) ……………………8
九、 研究目的 …………………………………………………10

第二章 材料與方法
一、 Y chromosome …………………………………………12
二、 系統環境需求 ……………………………………………12
三、 Microsatellite pattern algorithm …………………………13
四、 Microsatellite Component ………………………………13
五、 Microsatellite Profile System ……………………………14
六、 Microsatellite Embed System ……………………………17

第三章 結果
一、 Microsatellite Component ………………………………20
二、 Microsatellite Profile System ……………………………20
三、 Microsatellite Embed System ……………………………21

第四章 討論
一、 Microsatellite Component ………………………………23
二、 Microsatellite Profile System ……………………………24
三、 Microsatellite Embed System ……………………………25
四、 未來展望 …………………………………………………27

參考文獻 ………………………………………………………………29
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