Butyaev Alexander, Mavlyutov Ruslan, Blanchette Mathieu, Cudré-Mauroux Philippe, Waldispühl Jérôme
School Computer Science, McGill University, Canada.
eXascale InfoLab, University of Fribourg, Switzerland.
Nucleic Acids Res. 2015 Sep 18;43(16):e103. doi: 10.1093/nar/gkv476. Epub 2015 May 18.
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/.
近期发布的基因组三维（3D）结构有潜力改变我们对基因组的理解。尽管如此，存储技术和可视化工具仍需发展，以便为科学界提供对这些数据的快速便捷访问。我们同时推出了一个用于存储和查询三维基因组数据的数据库系统（3DBG），以及一个用于可视化和探索三维基因组结构的三维基因组浏览器（3DGB）。我们将3DBG与最先进的系统进行了基准测试，证明它比以前的解决方案更快，并且重要的是能够随着数据量的增加而优雅地扩展。我们还展示了我们的三维基因组网络浏览器在探索人类基因组结构方面的实用性。三维基因组浏览器可在http://3dgb.cs.mcgill.ca/获取。
