Evaluating the Structure Properties of DNA by Using the Spanning Tree Invariant of the Topological Markov Chain Model

應用拓樸馬可夫鏈模式展開樹不變量評估DNA序列之結構性質

謝俊逸(Jiunn-I Shieh) ； 李桂仁(Kuei-Jen Lee) ； 劉湘川(Hsiang-Chuan Liu) ； 曾杏園(Hsing-Yuan Tseng)

《測驗統計年刊》 15期_下 (2007/12) Pp. 53-62

https://doi.org/10.6773/JRMS.200712.0053

摘要

這項研究是使用一個拓樸馬可夫鏈模式從完全的基因組的去氧核糖核酸(DNA)序列順序中評估其架構性能的標準。在這項研究過程當中，我們選取4個細菌︰Halobacterium sp. NRC-1、Haloarcula marismortui、Campylobacter jejuni及Streptomyces coelicolor A3(2)，並應用拓樸馬可夫鏈模式之展開樹不變量進行序列評估。我們使用一個馬可夫鏈模型，建立一種框架模式，並利用選取的四種細菌的DNA序列去進行評估，分析其架構性能的特性及標準。我們相信基於不變量生成樹原理，我們能從生成樹的不變量中評估出在完全的基因組DNA序列架構中的隨機性(randomness)和緊密性(compactness)，而藉此種方法發現耐鹽性細菌的DNA序列特性。

關鍵字

拓樸馬可夫鏈模式 ； 展開樹不變量 ； DNA序列 ； 緊密性

並列摘要

In this study, four bacteria: Halobacterium sp. NRC-1, Haloarcula marismortui, Campylobacter jejuni, and Streptomyces coelicolor A3 (2), were investigated using the spanning tree invariant. This study used a topological Markov chain model to establish a framework to evaluate the level of structural properties of DNA from the complete genomic DNA sequences. Based upon the spanning tree invariant, we can evaluate the randomness and compactness of the complete genomic structures. Briefly, we discuss the correlations between GC contents and the values of spanning tree invariants.

並列關鍵字

topological Markov chain model ； spanning tree invariant ； DNA sequence ； compactness

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