nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning

作     者：Bader A.Alharbi Thamir H.Alshammari Nathan L.Felton Victor B.Zhurkin Feng Cui 

作者机构：Thomas H. Gosnell School of Life Sciences Rochester Institute of Technology B. Thomas Golisano College of Computing & Information Sciences Rochester Institute of Technology Information Technology Services Rochester Institute of Technology Laboratory of Cell Biology National Cancer Institute National Institutes of Health 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2014年第12卷第5期

页      面：249-253页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 090102[农学-作物遗传育种] 

基　　金：supported by the scholarship of the King Abdullah International Medical Research Center (KAIMRC) in Saudi Arabia to BA the start-up fund, Faculty of Development (FEAD) fund 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 

主　　题：Nucleosome rotational posi-tioning Sequence-dependent DNAanisotropy Prediction of nucteosomepositioning Sequence patterns Web server 

摘      要：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：//***. The user manual, implementation notes, description of the methodology and examples are available at the site.