Alharbi Bader A, Alshammari Thamir H, Felton Nathan L, Zhurkin Victor B, Cui Feng
Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA.
B. Thomas Golisano College of Computing & Information Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA.
Genomics Proteomics Bioinformatics. 2014 Oct;12(5):249-53. doi: 10.1016/j.gpb.2014.08.001. Epub 2014 Sep 16.
Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.
核小体定位对于基因表达至关重要，并且具有重大的生物学意义。通过实验绘制核小体排列的高昂成本表明需要采用计算方法来高分辨率预测核小体位置。在此，我们展示了一个基于网络的应用程序，通过分别实现用于核小体平移和旋转定位的两种模型（YR和W/S方案）来满足这一需求。我们的方法基于序列依赖性各向异性弯曲，它决定了DNA如何缠绕在组蛋白八聚体周围。该应用程序允许用户指定多种选项，如用于穿线计算的方案和参数，并提供多种布局格式。nuMap用Java/Perl/MySQL实现，可在http://numap.rit.edu上免费供公众使用。该网站提供用户手册、实现说明、方法描述和示例。
