nuMap:A Web Platform for Accurate Prediction of Nucleosome Positioning
10.1016/j.gpb.2014.08.001
- Author:
Alharbi A BADER
1
;
Alshammari H THAMIR
;
Felton L NATHAN
;
Zhurkin B VICTOR
;
Cui FENG
Author Information
1. Thomas H. Gosnell School of Life Sciences
- Keywords:
Nucleosome rotational posi-tioning;
Sequence-dependent DNA anisotropy;
Prediction of nucleosome positioning;
Sequence patterns;
Web server
- From:
Genomics, Proteomics & Bioinformatics
2014;(5):249-253
- CountryChina
- Language:Chinese
-
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 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.
