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A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

ABSTRACT: Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/.

SUBMITTER: Butyaev A

PROVIDER: S-EPMC4652742 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

Butyaev Alexander A Mavlyutov Ruslan R Blanchette Mathieu M Cudré-Mauroux Philippe P Waldispühl Jérôme J

Nucleic acids research 20150518 16

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and de ...[more]

PMID: 25990738

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