title: nuMap: a web platform for accurate prediction of nucleosome positioning.
abstract: 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.
authors.affiliation: Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA.
authors.forename: Bader A
authors.initials: BA
authors.lastname: Alharbi
authors.affiliation: B. Thomas Golisano College of Computing & Information Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA.
authors.forename: Thamir H
authors.initials: TH
authors.lastname: Alshammari
authors.affiliation: Information Technology Services, Rochester Institute of Technology, Rochester, NY 14623, USA.
authors.forename: Nathan L
authors.initials: NL
authors.lastname: Felton
authors.affiliation: Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Victor B
authors.initials: VB
authors.lastname: Zhurkin
authors.affiliation: Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA. Electronic address: fxcsbi@rit.edu.
authors.forename: Feng
authors.initials: F
authors.lastname: Cui
mesh_terms: D042002:Chromatin Assembly and Disassembly; D003198:Computer Simulation; D004247:DNA / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D009707:Nucleosomes / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D009707:Nucleosomes; D004247:DNA
keywords: Nucleosome rotational positioning; Prediction of nucleosome positioning; Sequence patterns; Sequence-dependent DNA anisotropy; Web server