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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
3D-GNOME: an integrated web service for structural modeling of the 3D genome
Przemyslaw Szalaj1, Paul J Michalski2, Przemysław Wróblewski3
1Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland Center for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland I-BioStat, Hasselt University, 3500 Hasselt, Belgium przemek.szalaj@uhasselt.be.
Abstract:
Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.
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