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物種演化距離計算之研究
魏至軒; Wei, Jr-shiuan 孫光天; Koun-Tem Sun; 數位學習科技學系 2007
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Title:
物種演化距離計算之研究
Author:
魏至軒
;
Wei, Jr-shiuan
孫光天
;
Koun-Tem Sun
;
數位學習科技學系
Subjects:
親緣分析
;
B 型肝炎病毒
;
突變率
;
演化率
;
演化公式
;
親緣樹
;
hepatitis B virus
;
mutation rate
;
evolutionary rate
;
evolutionary equation
;
phylogenetic analysis
;
phylogenetic tree
Description:
演化距離計算的應用方向主要是用在長期演化的親緣分析(phylogenetic analysis)和親緣樹(phylogenetic tree)的設計上,以往在此類長期的演化研究的分析,常會使用不合於實際情形的強假設,使計算方法只適用於某些的情況,如穩定性、非穩定性、同質性與異質性,本研究就是要建立一個能適用於穩定性、非穩定性、同質性與異質性的情形的方法。本研究分為兩個部份我們將JC 法分別修改成可運用於物種演化距離計算與B 型肝炎病毒序列長期突變率的估算兩個部份,第一個部份將修正後的物種演化距離計算公式-兩階段法(Two-Phasemethod)與JC、K2P、K3P、GTR、LogDet 等方法做比較,以證明本研究所提之修正公式效能。實驗結果顯示,本研究所設計之公式,在真實物種序列NCBI 資料庫之分析,正確性優於其他方法。第二個部份我們修改JC 法應用在B 型肝炎病毒序列的突變率計算上,讓其計算可由短期(一年)的演化可推估長期(四十年)的演化,結果發現與其它學者研究文獻的真實四十年的演化數據相似。實驗結果證明本研究之方法有極高正確性與彈性,將可成為生物資訊在物種親緣分析上一有用之技術。
The application of estimating evolutionary rates methods is usually on phylogenetic analysis orphylogenetic tree. These analyses are long-time evolution, but they always apply to someassumptions which don’t conform to all kinds of situations. The point in our study is to derive anew method for estimating evolutionary rates which adapts to geneneral situations. There are twosections in our research. Firstly, we apply our new method TP(Two-Phase) and JC、K2P、K3P、GTR、LogDet ...,etc to build phylogenetic tree with real taxas DNA sequences from NCBI database,and then we compare the results to prove TP for estimating evolutionary rates is better then others.Secondly, we apply a new estimating evolutionary rates method by modifying JC method forcalculating the HBV(hepatitis B virus); moreover, we use it to predict the long-term (40 years)mutation rate by the short time sequence data (one year). In a consequence, we find the results aresimilar to research reference by analyzing the real clinical sequence data, and TP for estimatingevolutionary rates is high accuracy and tolerance. The study would become an useful technology tophylogenetic analysis of bioinformatics.
碩士
Creation Date:
2007
Format:
121 bytes
text/html
Language:
中文
Identifier:
http://nutnr.lib.nutn.edu.tw/handle/987654321/3896
Source:
NUTN IR
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