Greenbaum Jason A, Pang Bo, Tullius Thomas D
Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.
Genome Res. 2007 Jun;17(6):947-53. doi: 10.1101/gr.6073107.
Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relational database, ORChID (OH Radical Cleavage Intensity Database), that contains extensive hydroxyl radical cleavage data produced from two DNA libraries. We have used the ORChID database to develop a set of algorithms that are capable of predicting the hydroxyl radical cleavage pattern of a DNA sequence of essentially any length, to high accuracy. We have used the prediction algorithm to produce a structural map of the 30 Mb of the ENCODE regions of the human genome.
目前几乎没有方法可用于绘制整个基因组中DNA的局部结构。羟基自由基切割模式是双链DNA溶剂可及表面积局部变化的一种度量，因此可提供有关DNA局部形状和结构的信息。我们报告了一个关系数据库ORChID（羟基自由基切割强度数据库）的构建，该数据库包含从两个DNA文库产生的大量羟基自由基切割数据。我们使用ORChID数据库开发了一组算法，这些算法能够高精度地预测基本上任何长度的DNA序列的羟基自由基切割模式。我们已使用该预测算法生成了人类基因组ENCODE区域30 Mb的结构图。
