BactoGeNIE: A large-scale comparative genome visualization for big displays

Aurisano, Jillian; Reda, Khairi; Johnson, Andrew; Marai, Elisabeta G.; Leigh, Jason

doi:10.1186/1471-2105-16-s11-s6

Title: BactoGeNIE: A large-scale comparative genome visualization for big displays

Journal Article · Thu Aug 13 00:00:00 EDT 2015 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-16-s11-s6· OSTI ID:1261160

Aurisano, Jillian ^[1]; Reda, Khairi ^[2]; Johnson, Andrew ^[1]; Marai, Elisabeta G. ^[1]; Leigh, Jason ^[3]

Univ. of Illinois, Chicago, IL (United States)
Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Hawai'i at Manoa, Honolulu, HI (United States)
Univ. of Hawai'i at Manoa, Honolulu, HI (United States)

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF)

Grant/Contract Number:: CNS-0959053; OCI-0943559; NSF CAREER IIS-1541277

OSTI ID:: 1261160

Journal Information:: BMC Bioinformatics, Vol. 16, Issue Suppl 11; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 6 works

Citation information provided by
Web of Science

References (17)

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes Fong, Christine; Rohmer, Laurence; Radey, Matthew BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-170	journal	January 2008
Visualizing genomes: techniques and challenges Nielsen, Cydney B.; Cantor, Michael; Dubchak, Inna Nature Methods, Vol. 7, Issue S3 https://doi.org/10.1038/nmeth.1422	journal	February 2010
SynView: a GBrowse-compatible approach to visualizing comparative genome data Wang, H.; Su, Y.; Mackey, A. J. Bioinformatics, Vol. 22, Issue 18 https://doi.org/10.1093/bioinformatics/btl389	journal	July 2006
SynBrowse: a synteny browser for comparative sequence analysis Pan, X.; Stein, L.; Brendel, V. Bioinformatics, Vol. 21, Issue 17 https://doi.org/10.1093/bioinformatics/bti555	journal	June 2005
Sequence Surveyor: Leveraging Overview for Scalable Genomic Alignment Visualization Albers, D.; Dewey, C.; Gleicher, M. IEEE Transactions on Visualization and Computer Graphics, Vol. 17, Issue 12 https://doi.org/10.1109/tvcg.2011.232	journal	December 2011
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements Darling, A. C. E. Genome Research, Vol. 14, Issue 7 https://doi.org/10.1101/gr.2289704	journal	June 2004
The use of gene clusters to infer functional coupling Overbeek, R.; Fonstein, M.; D'Souza, M. Proceedings of the National Academy of Sciences, Vol. 96, Issue 6 https://doi.org/10.1073/pnas.96.6.2896	journal	March 1999
Beyond visual acuity: the perceptual scalability of information visualizations for large displays Yost, Beth; Haciahmetoglu, Yonca; North, Chris Proceedings of the SIGCHI Conference on Human Factors in Computing Systems - CHI '07 https://doi.org/10.1145/1240624.1240639	conference	January 2007
MizBee: A Multiscale Synteny Browser Meyer, M.; Munzner, T.; Pfister, H. IEEE Transactions on Visualization and Computer Graphics, Vol. 15, Issue 6 https://doi.org/10.1109/tvcg.2009.167	journal	November 2009
Hybrid-Image Visualization for Large Viewing Environments Isenberg, Petra; Dragicevic, Pierre; Willett, Wesley IEEE Transactions on Visualization and Computer Graphics, Vol. 19, Issue 12 https://doi.org/10.1109/tvcg.2013.163	journal	December 2013
Information visualization on large, high-resolution displays: Issues, challenges, and opportunities Andrews, Christopher; Endert, Alex; Yost, Beth Information Visualization, Vol. 10, Issue 4 https://doi.org/10.1177/1473871611415997	journal	August 2011
Visualizing Large, Heterogeneous Data in Hybrid-Reality Environments Reda, K.; Febretti, A.; Knoll, A. IEEE Computer Graphics and Applications, Vol. 33, Issue 4 https://doi.org/10.1109/mcg.2013.37	journal	July 2013
Space to think: large high-resolution displays for sensemaking Andrews, Christopher; Endert, Alex; North, Chris the 28th international conference, p. 55-64 https://doi.org/10.1145/1753326.1753336	conference	January 2010
CD-HIT Suite: a web server for clustering and comparing biological sequences Huang, Ying; Niu, Beifang; Gao, Ying Bioinformatics, Vol. 26, Issue 5 https://doi.org/10.1093/bioinformatics/btq003	journal	January 2010
Gene-RiViT: A visualization tool for comparative analysis of gene neighborhoods in prokaryotes Price, Adam; Kosara, Robert; Gibas, Cynthia 2012 IEEE Symposium on Biological Data Visualization (BioVis) https://doi.org/10.1109/biovis.2012.6378593	conference	October 2012
A Nested Model for Visualization Design and Validation Munzner, Tamara IEEE Transactions on Visualization and Computer Graphics, Vol. 15, Issue 6 https://doi.org/10.1109/tvcg.2009.111	journal	November 2009
Effects of Display Size and Resolution on User Behavior and Insight Acquisition in Visual Exploration Reda, Khairi; Johnson, Andrew E.; Papka, Michael E. Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems https://doi.org/10.1145/2702123.2702406	conference	April 2015

Cited By (1)

Tasks, Techniques, and Tools for Genomic Data Visualization Nusrat, S.; Harbig, T.; Gehlenborg, N. Computer Graphics Forum, Vol. 38, Issue 3 https://doi.org/10.1111/cgf.13727	journal	June 2019

Similar Records

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

Journal Article · Tue Jan 01 00:00:00 EST 2013 · BMC Genomics · OSTI ID:1261160

Novichkov, Pavel S.; Kazakov, Alexey E.; Ravcheev, Dmitry A.; +8 more

Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

Technical Report · Thu May 26 00:00:00 EDT 2011 · OSTI ID:1261160

Baliga, Nitin S

GMT: A deep learning approach to generalized multivariate translation for scientific data analysis and visualization

Journal Article · Tue Apr 11 00:00:00 EDT 2023 · Computers and Graphics · OSTI ID:1261160

Yao, Siyuan; Han, Jun; Wang, Chaoli

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
comparative Genomics
large displays
visualization

Title: BactoGeNIE: A large-scale comparative genome visualization for big displays

Citation Formats

References (17)

Cited By (1)

Similar Records

Related Subjects