3DChrom

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Reconstructing three-dimensional structures of chromatins and TADs using Hi-C data and multidimensional scaling (MDS) (help page).

Email:

Paste a symmetric Hi-C interaction matrix (size <= 1000×1000, an example can be found here):

Or upload a matrix file:

Objective function

PASTIS

ChromSDE

self-defined with R equal to maximum distance

self-defined with R equal to shortest path

Note: please see help page for details of the four objective functions.

Submit

Download

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Source code for 3DChrom can be downloaded here.

References

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1. Tong Liu and Zheng Wang. Measuring the three-dimensional structural properties of topologically associating domains. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018, pp. 21-28: IEEE. (acceptance rate: 19.66%).

2. Liu, T., Wang, Z. Exploring the 2D and 3D structural properties of topologically associating domains. BMC Bioinformatics 20, 592 (2019) doi:10.1186/s12859-019-3083-z.

Contact

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For any questions or suggestions, please contact:
Dr. Zheng Wang
Department of Computer Science
University of Miami