Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.
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DOI：
10.1186/1471-2105-7-447
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发表时间：
2006-10-12
影响因子：
3
通讯作者：
Luo J
中科院分区：
文献类型：
--
作者：
Wang X;Shi X;Li Z;Zhu Q;Kong L;Tang W;Ge S;Luo J
染色体同源性的鉴定将揭示基因组进化中DNA复制、重排和丢失等奥秘。几种方法已经发展到检测染色体同源性的基础上的基因共线或共线。然而，先前报道的实现缺乏统计推断，而统计推断对于揭示实际的同源性是必不可少的。在这项研究中，我们提出了一种基于基因共线性的统计方法来检测同源染色体片段。我们在软件包ColinearScan中实现了这种方法，以使用动态规划算法检测假定的共线性区域。提出了统计模型来估计适当的参数值和评估假定的同源区域的重要性。统计推理、高计算效率和输入数据类型的灵活性是该方法的三个关键特征。我们对拟南芥和水稻基因组应用ColinearScan来检测每个物种内的重复区域以及这两个物种之间的同源片段。我们在水稻基因组中发现了比以前报道的更多的同源染色体片段。我们还发现水稻和拟南芥基因组之间有许多小的共线片段。
The identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homology based on gene synteny or colinearity. However, the previously reported implementations lack statistical inferences which are essential to reveal actual homologies. In this study, we present a statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a dynamic programming algorithm. Statistical models are proposed to estimate proper parameter values and evaluate the significance of putative homologous regions. Statistical inference, high computational efficiency and flexibility of input data type are three key features of our approach. We apply ColinearScan to the Arabidopsis and rice genomes to detect duplicated regions within each species and homologous fragments between these two species. We find many more homologous chromosomal segments in the rice genome than previously reported. We also find many small colinear segments between rice and Arabidopsis genomes.
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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
30.8
作者：
McLysaght, A;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
DOI：
10.1142/s0219720004000892
发表时间：
2004-12-01
影响因子：
1
作者：
Bourque, Guillaume;Sankoff, David
通讯作者：
Sankoff, David
影响因子：
1.9
作者：
Li, H;Liu, JS;Hao, BL
通讯作者：
Hao, BL
影响因子：
4
作者：
Simillion, C;Vandepoele, K;Van de Peer, Y
通讯作者：
Van de Peer, Y