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GSDB : Genome Structure Database

Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory,

University of Missouri, Columbia MO 65211

Contact:

             Jianlin Cheng, PhD
             Department of Computer Science
             University of Missouri, Columbia
             Email: [email protected]

GSDB is a database of Hi-C data chromosome and genome structures. Our goal is that this database will enable the exploration of the dynamic architecture of the different Hi-C 3D structure in a variety of cells and tissues.

Over 50,000 structures from 12 start-of-the-art Hi-C data structure prediction algorithms for 32 Hi-C datasets each containing varying resolutions.

1. Content of folders:

  • src: source code for the website
  • GSDB_Scripts: Contains the Algorithms and the scripts used for data extraction, data normalization, and 3D structure generation.
  • Database Data Info.xlsx: Contains more information about the Hi-C data and the 3D structure prediction tools
  • ID_Generator.jar: Java executable file to create the GSDB ID. To execute type in terminal: java -jar ID_Generator.jar

2. Algorithms Input

For each algorithm, we have described the contact matrix input format they accept and the input file name extension/suffix used for the 3D structure Construction

Algorithm Input Format GSDB Input filename suffix
LorDG 3-column Matrix _list.txt
3DMax 3-column Matrix _list.txt
MOGEN 3-column Matrix _list.txt
Pastis 3-column Matrix(bin1,bin2,IF), and mapping coordinate(chr, start_pos,end_pos, bin) .n_contact, .cbins
Chromosome3D n x n Square Matrix _matrix.txt
HSA 2-column bin positon with n x n Square Matrix _HSA.txt
miniMDS Chromosome,positon,IF(chr,start_pos1,end_pos1,chr, start_pos2,end_pos2,IF) .bed
ShRec3D n x n Square Matrix _matrix.txt
GEM 2-column bin positon with n x n Square Matrix _HSA.txt
ChromSDE 3-column Matrix, and mapping coordinate .n_contact, .cbins
SIMBA3D n x n Square Matrix .npy
InfMod3DGen n x n Square Matrix _matrix.txt

3. Disclaimer

The executable software and the source code of is distributed free of charge as it is to any non-commercial users. The authors hold no liabilities to the performance of the program.