Sequence surveyor: Leveraging overview for scalable genomic alignment visualization

IEEE Transactions on Visualization and Computer Graphics

Volumn 17, Issue 12, 2011, Pages 2392-2401

  Albers, Danielle ^a   Dewey, Colin ^a   Gleicher, Michael ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Bioinformatics Visualization; Perception Theory; Scalability Issues; Visual Design

Indexed keywords

AGGREGATION SCHEMES; DATA DISTRIBUTION; DATA SETS; ENCODINGS; GENOME ALIGNMENT; GENOMIC-SEQUENCE DATA; GLOBAL TRENDS; LARGE DATA; MULTIPLE GENOME ALIGNMENT; PROBLEM SCALE; SCALABILITY ISSUES; SEQUENCE ALIGNMENTS; SIGNAL PROCESSING THEORY; VISUAL DESIGN; VISUALIZATION TECHNIQUE; VISUALIZATION TOOLS;

ALIGNMENT; BIOINFORMATICS; DESIGN; GENES; SIGNAL PROCESSING; SURVEYING; VISUALIZATION;

DATA VISUALIZATION;

ARTICLE; BACTERIAL GENOME; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETIC DATABASE; GENOMICS; HUMAN; MOLECULAR EVOLUTION; SEQUENCE ALIGNMENT; STATISTICS; VISION;

COMPUTER GRAPHICS; COMPUTER SIMULATION; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; GENOMICS; HUMANS; SEQUENCE ALIGNMENT; SOFTWARE; USER-COMPUTER INTERFACE; VISUAL PERCEPTION;

EID: 80955157806     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2011.232     Document Type: Article

References (34)

1. G. A. Alvarez, T. Konkle, and A. Oliva. Searching in dynamic displays: Effects of configural predictability and spatiotemporal continuity. Journal of Vision, 7(14):1-12, 2007.
2. R. Arnheim. The Perception of Maps. Cartography and Geographic Information Science, 3(1):5-10, Apr. 1976.
3. B. Balas, L. Nakano, and R. Rosenholtz. A summary-statistic representation in peripheral vision explains visual crowding. Journal of Vision, 9(12):1-18, 2009.
4. C. A. Brewer, G. W. Hatchard, and M. A. Harrower. Colorbrewer in print: A catalog of color schemes for maps. Cartography and Geographic Information Science, 30:5-32(28), 2003. (Pubitemid 36463771)
5. T. J. Carver, K. M. Rutherford, M. Berriman, M.-A. Rajandream, B. G. Barrell, and J. Parkhill. ACT: the Artemis comparison tool. Bioinformatics, 21(16):3422-3423, 2005. (Pubitemid 41222448)
6. M. Clamp, J. Cuff, S. M. Searle, and G. J. Barton. The Jalview Java alignment editor. Bioinformatics (Oxford, England), 20(3):426-7, 2004. (Pubitemid 38262778)
7. A. C. E. Darling, B.Mau, F. R. Blattner, and N. T. Perna. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res, 14(7):1394-1403, 2004. (Pubitemid 39029237)
8. C. Duran, Z. Boskovic,M. Imelfort, J. Batley, N. A. Hamilton, and D. Edwards. CMap3D: a 3D visualization tool for comparative genetic maps. Bioinformatics (Oxford, England), 26(2):273-4, 2010.
9. R. Engels, T. Yu, C. Burge, J. P. Mesirov, D. DeCaprio, and J. E. Galagan. Combo: a whole genome comparative browser. Bioinformatics, 22(14):1782-1783, 2006. (Pubitemid 44288342)
10. J.-D. Fekete and C. Plaisant. Interactive information visualization of a million items. IEEE Symposium on Information Visualization, pages 117-124, 2002.
11. S. L. Franconeri. The nature and status of visual resources. In D. Resiberg, editor, Oxford Handbook of Cognitive Psychology. Oxford University Press, 2011.
12. K. A. Frazer, L. Pachter, A. Poliakov, E. M. Rubin, and I. Dubchak. VISTA: computational tools for comparative genomics. Nucleic Acids Research, 32:W273-9, 2004. (Pubitemid 38997343)
13. M. G. Grabherr, P. Russell, M. Meyer, E. Mauceli, J. Alf̈oldi, F. Di Palma, and K. Lindblad-Toh. Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics (Oxford, England), 26(9):1145-51, 2010.
14. J. R. Grant and P. Stothard. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Research, 36(suppl 2):W181-W184, 2008.
15. L. Guy, J. Roat Kultima, and S. G. E. Andersson. genoPlotR: comparative gene and genome visualization in R. Bioinformatics (Oxford, England), 26(18):2334-2335, 2010.
16. H. Hagh-Shenas, S. Kim, V. Interrante, and C. Healey. Weaving versus blending: a quantitative assessment of the information carrying capacities of two alternative methods for conveying multivariate data with color. IEEE Transactions on Visualization and Computer Graphics, 13(6):1270-7, 2007. (Pubitemid 350076599)
17. C. Healy. Perception in visualization. Web Resource, http://wwwisc.ncsu. edu/faculty/healey/PP/index.html.
18. P. Husemann and J. Stoye. R2Cat: Synteny Plots and Comparative Assembly. Bioinformatics (Oxford, England), 26(4):570-1, 2010.
19. D. Jen, L. Larson, C. Stolte, D. DeCaprio, T. Allen, B. Birren, M. Koehrsen, and M. Henn. Comparative viral genome visualization. IEEE InfoVis Poster Proceedings, 2009.
20. D. A. Keim. Designing pixel-oriented visualization techniques: Theory and applications. IEEE Transactions on Visualization and Computer Graphics, 6:59-78, 2000. (Pubitemid 30594716)
21. W. J. Kent, C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, and D. Haussler. The Human Genome Browser at UCSC. Genome Research, 12(6):996-1006, 2002. (Pubitemid 34662293)
22. M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne, D. Horsman, S. J. Jones, and M. A. Marra. Circos: an information aesthetic for comparative genomics. Genome research, 19(9):1639-45, Sept. 2009.
23. D. Lee, J.-H. Choi, M.M. Dalkilic, and S. Kim. COMPAM: visualization of combining pairwise alignments for multiple genomes. Bioinformatics, 22(2):242-244, 2006. (Pubitemid 43205413)
24. M. Meyer, T. Munzner, and H. Pfister. Mizbee: A multiscale synteny browser. IEEE Transactions on Visualization and Computer Graphics, 15:897-904, 2009.
25. J.-B. Michel, Y. K. Shen, A. P. Aiden, A. Veres, M. K. Gray, T. G. B. Team, J. P. Pickett, D. Hoiberg, D. Clancy, P. Norvig, J. Orwant, S. Pinker, M. A. Nowak, and E. L. Aiden. Quantitative analysis of culture using millions of digitized books. Science, 331(6014):176-182, 2011.
26. M. Muffato, A. Louis, C.-E. Poisnel, and H. R. Crollius. Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics (Oxford, England), 26(8):1119-21, Apr. 2010.
27. T. Peeters, M. Fiers, H. van de Wetering, J.-P. Nap, and J. J. van Wijk. Case Study: Visualization of annotated DNA sequences. Eurographics, 2004.
28. J. B. Procter, J. Thompson, I. Letunic, C. Creevey, F. Jossinet, and G. Barton. Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods, 7(3):S16-S25, 2010.
29. R. Rosenholtz, Y. Li, and L. Nakano. Measuring visual clutter. Journal of Vision, 7(2):171-1722, 2007.
30. B. Shneiderman. Extreme visualization: squeezing a billion records into a million pixels. In Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data, pages 3-12, New York, NY, USA, 2008. ACM.
31. J. Slack, K. Hildebrand, T. Munzner, and K. John. SequenceJuxtaposer: Fluid navigation for large-scale sequence comparison in context. In German Conference on Bioinformatics, pages 37-42, 2004.
32. A. Slingsby, J. Dykes, and J. Wood. Configuring hierarchical layouts to address research questions. IEEE Transactions on Visualization and Computer Graphics, 15(6):977-984, 2009.
33. B. Swihart, B. Caffo, B. James, M. Strand, B. Schwartz, and N. Punjabi. Lasagna plots: A saucy alternative to spaghetti plots. Epidemiology, 21(5):621-625, 2010.
34. M. Wattenberg and F. Viegas. Beautiful history: Visualizing wikipedia. In J. Steele and N. Illinsky, editors, Beautiful Visualization, page 416. O'Reilly Media, Inc., 2010.