- Unique identifier:
- Web user interface
- Input data:
- 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.
- Database management system:
- 3D GeNOme Modeling Engine
- Restrictions to use:
- Programming languages:
- Computer skills:
- Documentation: http://3dgnome.cent.uw.edu.pl/tutorial/
- Przemek Szałaj <>
No open topic.
(Szalaj et al., 2016)
3D-GNOME: an integrated web service for structural modeling of the 3D genome.
Nucleic Acids Res.
PMID: 27185892 DOI: 10.1093/nar/gkw437
(Tang et al., 2015)
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.
PMID: 26686651 DOI: 10.1016/j.cell.2015.11.024
Centre of New Technologies, University of Warsaw, Warsaw, Poland; Center for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland; I-BioStat, Hasselt University, Hasselt, Belgium; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
National Leading Research Centre in Bialystok; European Union under the European Social Fund; Polish National Science Centre [2014/15/B/ST6/05082, 2013/09/B/NZ2/00121]; European Cooperation in Science and Technology action [COST BM1405, BM1408]; Director Innovation Fund from Jackson Laboratory and NCI [R01 CA186714]; The Roux family as a Florine Roux Endowed Chair and Professor in Genomics and Computational Biology
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