Delineating relative homogeneous G+C domains in DNA sequences
Delineating relative homogeneous G+C domains in DNA sequences
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DOI：
10.1016/s0378-1119(01)00672-2
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发表时间：
2001-10-03
期刊：
影响因子：
3.5
通讯作者：
Li, WT
中科院分区：
文献类型：
--
作者：
Li, WT
G + C内容同质性的概念总是相对的、主观的。这一点是强调和量化，本文使用一个简单的例子，一个序列分割成两个连续性。序列是否是同质的，可以通过两个子序列模型是否比一个序列模型更好地描述DNA序列来回答。至少有三种等价的方法来看待1到2的分割：詹森-香农散度度量，对数似然比检验和使用贝叶斯信息准则的模型选择。一旦选择了标准，DNA序列就可以递归地分割成多个域。我们使用一个主观的标准，称为分割强度的基础上贝叶斯信息准则。一个序列是否是齐次的以及它有多少个定义域取决于这个标准。我们比较了六个不同的基因组序列（酵母S。酿酒酵母染色体III和IV，细菌M. pneumoniae，人主要组织相容性复合体序列，人染色体21和22中最长的重叠群）。通过递归分割的结果证实，酵母染色体IV比酵母染色体III更均一，人类染色体21比人类染色体22更均一，并且细菌基因组可能由于具有不同碱基组成的短片段而不是均一的。递归分割也提供了一个定量的标准，以确定在人类序列中的isochore。我们的递归分割的一些功能，如准确划定域边界的可能性，是上级的移动窗口的方法通常用于这种分析。(C)2001爱思唯尔科技有限公司。保留所有权利。
The concept of homogeneity of G + C content is always relative and subjective. This point is emphasized and quantified in this paper using a simple example of one sequence segmented into two subsequences. Whether the sequence is homogeneous or not can be answered by whether the two-subsequence model describes the DNA sequence better than the one-sequence model. There are at least three equivalent ways of looking at the 1-to-2 segmentation: Jensen-Shannon divergence measure, log likelihood ratio test, and model selection using Bayesian information criterion. Once a criterion is chosen, a DNA sequence can be recursively segmented into multiple domains. We use one subjective criterion called segmentation strength based on the Bayesian information criterion. Whether or not a sequence is homogeneous and how many domains it has depend on this criterion. We compare six different genome sequences (yeast S. cerevisiae chromosome III and IV, bacterium M. pneumoniae, human major histocompatibility complex sequence, longest contigs in human chromosome 21 and 22) by recursive segmentations at different strength criteria. Results by recursive segmentation confirm that yeast chromosome IV is more homogeneous than yeast chromosome III, human chromosome 21 is more homogeneous than human chromosome 22, and bacterial genomes may not be homogeneous due to short segments with distinct base compositions. The recursive segmentation also provides a quantitative criterion for identifying isochores in human sequences. Some features of our recursive segmentation, such as the possibility of delineating domain borders accurately, are superior to those of the moving-window approach commonly used in such analyses. (C) 2001 Elsevier Science B.V. All rights reserved.