Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal o...
| Autores: | , , , , , , , , , , , , , |
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| Tipo de recurso: | artículo |
| Fecha de publicación: | 2019 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/191923 |
| Acceso en línea: | https://hdl.handle.net/2117/191923 https://dx.doi.org/10.1093/nar/gkz759 |
| Access Level: | acceso abierto |
| Palabra clave: | Computational biology Bioinformatics Epigenetics Chromatin Computational methods Genomics Nucleosome Dynamics Nucleosome architecture Bioinformàtica Genòmica -- Informàtica ADN Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica |
| Sumario: | We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models. |
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