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

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 simultaneou...

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Detalles Bibliográficos
Autores principales: Butyaev, Alexander, Mavlyutov, Ruslan, Blanchette, Mathieu, Cudré-Mauroux, Philippe, Waldispühl, Jérôme
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Methods Online
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652742/
https://www.ncbi.nlm.nih.gov/pubmed/25990738
http://dx.doi.org/10.1093/nar/gkv476
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author Butyaev, Alexander
Mavlyutov, Ruslan
Blanchette, Mathieu
Cudré-Mauroux, Philippe
Waldispühl, Jérôme
author_facet Butyaev, Alexander
Mavlyutov, Ruslan
Blanchette, Mathieu
Cudré-Mauroux, Philippe
Waldispühl, Jérôme
author_sort Butyaev, Alexander
collection PubMed
description 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/.
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spelling pubmed-46527422015-11-25 A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data Butyaev, Alexander Mavlyutov, Ruslan Blanchette, Mathieu Cudré-Mauroux, Philippe Waldispühl, Jérôme Nucleic Acids Res Methods Online 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/. Oxford University Press 2015-09-18 2015-05-18 /pmc/articles/PMC4652742/ /pubmed/25990738 http://dx.doi.org/10.1093/nar/gkv476 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Online
Butyaev, Alexander
Mavlyutov, Ruslan
Blanchette, Mathieu
Cudré-Mauroux, Philippe
Waldispühl, Jérôme
A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data
title A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data
title_full A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data
title_fullStr A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data
title_full_unstemmed A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data
title_short A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data
title_sort low-latency, big database system and browser for storage, querying and visualization of 3d genomic data
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652742/
https://www.ncbi.nlm.nih.gov/pubmed/25990738
http://dx.doi.org/10.1093/nar/gkv476
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