基于DNA序列4D表示的相似性分析与进化树算法研究

【作者】 李刚成；

【导师】 廖国华；

【作者基本信息】 中南大学 ， 模式识别与智能系统， 2008， 硕士

【摘要】 随着人类基因组计划的开展,以及各种生物基因序列的研究,产生了越来越多的分子序列数据。对这些序列数据进行科学的分析、处理推动了生物信息学的发展。随着基因序列的增长,基因序列的图形表达方法已成为研究基因序列的重要手段,如何给出有效的基因序列图形表达方式并在此基础上对基因的分类以及基因进化关系进行分析是生物信息学中一个热门课题。本文在DNA序列图形表示方法、生物序列的相似性分析及进化树构建算法方面进行研究。本文给出了一个关于DNA序列的图形表示方法较为详细的综述,其中先从简单的2维表示方法入手,然后在2维表示方法的基础上介绍了3维的图形表示方法,最后给出了高维的表示方法。然而,论文的中心内容并不仅限于图形表示方法的研究,而是从基于图形表示的数值特征向量去进行DNA序列之间的相似性分析。在接下来的四、五章中,给出了作者提出的基于核苷酸物理化学性质的新表示方法和序列之间相似性分析。以11种生物的β-globin基因的第一外显子为例分析了序列间的相似性,并同其它文献中的相似性分析的结果进行了比较。在文章最后,简单介绍了作为DNA序列比较的一个应用——构造系统发生树,提出了最大树模糊聚类方法构造系统发生树。更多还原

【Abstract】 With the development of HGP (human genome project), the research on different species gene sequences, more and more molecular sequences data have been generated. The need to analyze, process these data accelerates the development of Bioinformatics. With the increasing of gene sequences, the graphical representation is becoming important for studing gene sequences. So how to give effective graphical representation of gene sequences, to classify genes, and to study the phylogenetic relationships are the important problems in Bioinformatics.This dissertation mainly studied the graphical representation of DNA sequence, the similarity analysis of biological sequences and the algorithm for constructing the phylogenetic tree.In this paper, we first presented on graphical representations of the DNA sequence in more detail, in which we start with a simple two-dimensional graphical representation method, and then based on the two-dimensional representation put forward three-dimensional graphic representation, and finally give a high-dimensional representation. However, the focus of this thesis is not only to introduce the methods of study of graphical representations but also to describe several numerical analysis methods based on graphical representations for the comparison of different DNA sequences. In the next four to five chapters, the author proposed a new graphical representation method based on the nucleotide physical and chemical properties, and similarity analysis of DNA sequences. Moreover, we illustrated the method by examining similarity or dissimilarity of exon-1 ofβ-globin gene of 11 species, and compared our results with some existing results of other methods. Finally, we briefly introduced one application of comparison of the DNA sequence -constructing phylogenetic tree. Lastly we propose a fuzzy clustering method of largest tree structing phylogenetic tree.更多还原