This is the Windows app named Gen3D whose latest release can be downloaded as gen3d.cpp. It can be run online in the free hosting provider OnWorks for workstations.
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SCREENSHOTS
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Gen3D
DESCRIPTION
Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts.
The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224).
If you use Gen3D in your research, please cite:
Nowotny, Jackson, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare, Hannah Chen, Noelan Hensley, Tuan Trieu, Renzhi Cao, and Jianlin Cheng. "Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data." BMC bioinformatics 16, no. 1 (2015): 338.
Features
- Use chromosomal contact data acquired using the Hi-C technique
- Construct 3D structural genome and chromosome models from chromosomal contact data
- Initialize the coordinates using probabilistic approach
- Novel method to represent satisfied contacts in heat map matrix
- Scoring schemes to figure out long range and short range contacts
- Compared with other existing method and also validated with genome features
Audience
Science/Research, Engineering
Programming Language
C++
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/gen3d/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
