This is the Linux app named Gen3D to run in Linux online 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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Gen3D to run in Linux online
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++
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.
