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. 2015 Sep 18;43(16):e103.
doi: 10.1093/nar/gkv476. Epub 2015 May 18.

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

Alexander Butyaev  1 , Ruslan Mavlyutov  2 , Mathieu Blanchette  1 , Philippe Cudré-Mauroux  3 , Jérôme Waldispühl  4
Affiliations

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

Alexander Butyaev et al. Nucleic Acids Res. .

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/.

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Figures

Figure 1.
Figure 1.
Overall architecture of 3DBG.
Figure 2.
Figure 2.
Sample screenshot of 3DGB.
Figure 3.
Figure 3.
Comparison of 3DBG and PostGIS query latencies. The x-axis shows the number of records returned and the y-axis shows the latency in milliseconds (ms). Red dots are 3DBG data and blue dots PostGIS data.
Figure 4.
Figure 4.
Dependencies of 3DBG and PostGIS latencies with query size. The x-axis shows the number of records returned and the y-axis shows the latency in milliseconds (ms). 3DBG data are represented with full lines, and PostGIS data with dotted lines. The colors of the curves are associated with the different sizes of the query (edge sizes of the cube varying from 100 to 400 base units). The latency threshold for real-time visualization (200 ms) is indicated with a horizontal red line.
Figure 5.
Figure 5.
Comparison of 3DBG and HBase query latencies. The x-axis shows the number of record returned and the y-axis the latency in milliseconds (ms).
See this image and copyright information in PMC

References

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