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 nucle...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 param- eters 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.展开更多
基金supported by the scholarship of the King Abdullah International Medical Research Center (KAIMRC) in Saudi Arabia to BAthe start-up fund, Faculty of Development (FEAD) fund+1 种基金Dean’s Research Initiation Grant (D-RIG) fund of Rochester Institute of Technology in the USA awarded to FC the Intramural Research Program of National Cancer Institute, NIH of the USA to VBZ
文摘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 param- eters 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.
