nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning

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 ful...

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Bibliographic Details
Published in:Genomics, proteomics & bioinformatics proteomics & bioinformatics, 2014-10, Vol.12 (5), p.249-253
Main Authors: Alharbi, Bader A., Alshammari, Thamir H., Felton, Nathan L., Zhurkin, Victor B., Cui, Feng
Format: Article
Language:English
Subjects:
Application Note
DNA
gene expression
histones
Internet
Nucleosome rotational positioning
nucleosomes
prediction
Prediction of nucleosome positioning
Sequence patterns
Sequence-dependent DNA anisotropy
translation (genetics)
Web server
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Summary: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.
ISSN:1672-0229
2210-3244
DOI:10.1016/j.gpb.2014.08.001