Dataset Information

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

ABSTRACT: Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community.

SUBMITTER: Kumar R

PROVIDER: S-EPMC5622372 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

Kumar Rajendra R Sobhy Haitham H Stenberg Per P Lizana Ludvig L

Nucleic acids research 20170901 17

Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by i ...[more]

PMID: 28973466

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Project description:Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and heritable phenotypic markers. It also provides graphical comparison of maps sharing the same markers as well as dot plot and correspondence matrices. MapViewer integrates directly with the Tripal application programming interface framework, improving data searching capability and providing a more seamless experience for site visitors. The Tripal MapViewer interface can be integrated in any Tripal map page and linked from any Tripal page for markers, QTLs, heritable morphological markers or genes. Configuration of the display is available through a control panel and the administration interface. The administration interface also allows configuration of the custom database query for building materialized views, providing better performance and flexibility in the way data is stored in the Chado database schema. MapViewer is implemented with the D3.js technology and is currently being used at the Genome Database for Rosaceae (https://www.rosaceae.org), CottonGen (https://www.cottongen.org), Citrus Genome Database (https://citrusgenomedb.org), Vaccinium Genome Database (https://www.vaccinium.org) and Cool Season Food Legume Database (https://www.coolseasonfoodlegume.org). It is also currently in development on the Hardwood Genomics Web (https://hardwoodgenomics.org) and TreeGenes (https://treegenesdb.org). Database URL: https://gitlab.com/mainlabwsu/tripal_map.

Dataset Information

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

Publications

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

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