gen3d

We have hosted the application gen3d in order to run this application in our online workstations with Wine or directly.

Quick description about gen3d:

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: