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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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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cited_by cdi_FETCH-LOGICAL-c5078-9830e2b3aab596851e2982275dd65de2d79351bcaeddb00b45945476230e372d3
cites cdi_FETCH-LOGICAL-c5078-9830e2b3aab596851e2982275dd65de2d79351bcaeddb00b45945476230e372d3
container_end_page 253
container_issue 5
container_start_page 249
container_title Genomics, proteomics & bioinformatics
container_volume 12
creator Alharbi, Bader A.
Alshammari, Thamir H.
Felton, Nathan L.
Zhurkin, Victor B.
Cui, Feng
description 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.
doi_str_mv 10.1016/j.gpb.2014.08.001
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source Oxford Journals Open Access Collection; PubMed Central
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
title nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning
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