Global visualization and alignments of whole bacterial genomes

IEEE Transactions on Visualization and Computer Graphics

Volumn 9, Issue 3, 2003, Pages 361-377

  Wong, Pak Chung ^a   Wong, Kwong Kwok ^b   Foote, Harlan ^a   Thomas, Jim ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Bioinformatics; Digital image processing; Fractal curve; Gestalt psychology; Visualization; Whole genome alignment

Indexed keywords

BACTERIA; BINARY SEQUENCES; DIGITAL FILTERS; FRACTALS; GENETIC ENGINEERING; INFORMATION TECHNOLOGY; RANDOM PROCESSES; RECURSIVE FUNCTIONS;

BACTERIAL GENOMES; BIOINFORMATICS; FRACTAL CURVE; GESTALT PSYCHOLOGY; GLOBAL VISUALIZATION; WHOLE GENOME ALIGNMENT;

IMAGE PROCESSING;

EID: 0042349283     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2003.1207444     Document Type: Article

References (38)

1. R.A. Alm, L.S. Ling, D.T. Moir, B.L. King, E.D. Brown, P.C. Doig, D.R. Smith, B. Noonan, B.C. Guild, B.L. deJonge, G. Carmel, P.J. Tummino, A. Caruso, M. Uria-Nickelsen, D.M. Mills, C. Ives, R. Gibson, D. Merberg, S.D. Mills, Q. Jiang, D.E. Taylor, G.F. Vovis, and T.J. Trust, "Genomic Sequence Comparison of Two Unrelated Isolates of the Human Gastric Pathogen Helicobacter Pylori," Nature, vol. 397, no. 6715, pp. 176-180, Jan. 1999.
2. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman, "Basic Local Alignment Search Tool," J. Molecular Biology, vol. 215, no. 3, pp. 403-410, 1990.
3. A.R. Butz, "Alternative Algorithm for Hilbert's Space-Filling Curve," IEEE Trans. Computers, vol. 20, no. 4, pp. 424-426, Apr. 1971.
4. S.K. Card, J.D. Mackinlay, and B. Shneiderman, Readings in Information Visualization-Using Vising to Think. Morgan Kaufmann, 1999.
5. E.H. Chi, P. Barry, E. Shoop, J.V. Carlis, E. Retzel, and J. Riedl, "Visualization of Biological Sequences Similarity Search Results," Proc. IEEE Visualization '95, pp. 44-51, Oct. 1995.
6. E.H. Chi, J. Riedl, E. Shoop, J.V. Carlis, E. Retzel, and P. Barry, "Flexible Information Visualization of Multivariate Data from Biological Sequence Similarity Searches," Proc. IEEE Visualization '96, pp. 133-140, Oct. 1996.
7. A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S. Salzberg, "Alignment of Whole Genomes," Nucleic Acids Research, vol. 27, no. 11, pp. 2369-2376, May 1999.
8. L. Florea, C. Riemer, S. Schwartz, Z. Zhang, N. Stojanovic, W. Miller, and M. McClelland, "Web-Based Visualization Tools for Bacterial Genome Alignments," Nucleic Acids Research, vol. 28, no. 18, pp. 3486-3496, Aug. 2000.
9. A.J. Gibbs and G.A. McIntyre, "The Diagram, a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences," European J. Biochemistry, vol. 16, pp. 1-11, 1970.
10. R.C. Gonzalez and R.E. Woods, Digital Image Processing, second ed. Prentice Hall, 2001.
11. E. Hamori and J. Ruskin, "H Curves, a Novel Method of Representation of Nucleotide Series Especially Suited for Long DNA Sequences," The J. Biological Chemistry, vol. 258, no. 2, pp. 1318-1327, July 1983.
12. http://www.stat.duke/edu/courses/sta1xx/Data_sets/data_sets.html, 2002.
13. http://www.gcg.com/products/macvector.html, 2002.
14. http://www.ncbi.nlm.nih.gov/, 2002.
15. http://www.tigr.org/tdb/mdb/mdb.html, 2002.
16. D. Jerding and J. Stasko, "The Information Mural: A Technique for Displaying and Navigating Large Information Spaces," IEEE Trans. Visualization and Computer Graphics, vol. 4, no. 3, pp. 257-271, July 1998.
17. S. Kalman, W. Mitchell, R. Marathe, C. Lammel, J. Fan, R.W. Hyman, L. Olinger, J. Grimwood, R.W. Davis, and R.S. Stephens, "Comparative Genomes of Chlamydia pneumoniae and C. trachomatis," Nature Genetics, vol. 21, no. 4, pp. 385-389, Apr. 1999.
18. D.A. Keim, "Designing Pixel-Oriented Visualization Techniques: Theory and Applications," IEEE Trans. Visualization and Computer Graphics, vol. 6, no. 1, Jan.-Mar. 2000.
19. D.A. Keim, H.-P. Kriegel, and T. Seidl, "Visual Feedback in Querying Large Databases," Proc. IEEE Visualization '93, pp. 158-165, Oct. 1993.
20. D.A. Keim, H.-P. Kriegel, and M. Ankerst, "Recursive Pattern: A Technique for Visualizing Very Large Amounts of Data," Proc. IEEE Visualization '95, pp. 279-286, Oct. 1995.
21. W. Kohler, Gastalt Psychology: An Introduction to New Concepts in Modern Psychology. Liveright, 1992.
22. A. Mamania, G. Grinstein, and K. Marx, "Visualization Techniques for Genomic DNA," Proc. SPIE '96 Visual Data Exploration and Analysis Conf., vol. 2656, pp. 189-199, 1996.
23. J. Parkhill, M. Achtman, K.D. James, S.D. Bentley, C. Churcher, S.R. Klee, G. Morelli, D. Basham, D. Brown, T. Chillingworth, R.M. Davies, P. Davis, K. Devlin, T. Feltwell, N. Hamlin, S. Holroyd, K. Jagels, S. Leather, S. Moule, K. Mungall, M.A. Quail, M.A. Rajandream, K.M. Rutherford, M. Simmonds, J. Skelton, S. Whitehead, B.G. Spratt, and B.G. Barrell, "Complete DNA Sequence of a Serogroup A Strain of N. Meningitidis Z2491," Nature, vol. 404, no. 6777, pp. 502-506, Mar. 2000.
24. W.R. Pearson, "Comparison of Methods for Searching Protein Sequence Databases," Protein Sciences, vol. 4, no. 6, pp. 1145-1160, June 1995.
25. H.-O. Peitgen, H. Jürgens, and D. Saupe, Chaos and Fractals-New Frontiers of Science. New York: Springer-Verlag, 1992.
26. J. Pustell and F.C. Kafatos, "A Convenient and Adaptable Package of Computer Programs for DNA and Protein Sequence Management, Analysis, and Homology Determination," Nucleic Acids Research, vol. 12, pp. 643-655, 1984.
27. T.D. Read, R.C. Brunham, C. Shen, S.R. Gill, J.F. Heidelberg, O. White, E.K. Hickey, J. Peterson, T. Utterback, K. Berry, S. Bass, K. Linher, J. Weidman, H. Khouri, B. Craven, C. Bowman, R. Dodson, M. Gwinn, W. Nelson, R. DeBoy, J. Kolonay, G. McClarty, S.L. Salzberg, J. Eisen, and C.M. Fraser, "Genome Sequences of Chlamydia Trachomatis MoPn and Chlamydia Pneumoniae AR39," Nucleic Acids Research, vol. 28, no. 6, pp. 1397-1406, June 2000.
28. S. Schwartz, Z. Zhang, K.A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miler, "PipMaker-A Web Server for Aligning Two Genomic DNA Sequences," Genome Research, vol. 10, no. 55, pp. 557-586, Apr. 2000.
29. M. Shirai, H. Hirakawa, M. Kimoto, M. Tabuchi, F. Kishi, K. Ouchi, T. Shiba, K. Ishii, M. Hattori, S. Kuhara, and T. Nakazawa, "Comparison of Whole Genome Sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA," Nucleic Acids Research, vol. 28, no. 12, pp. 2311-2314, June 2000.
30. M. Singer and P. Berg, Genes & Genomes. Univ. Science Book, 1991.
31. E.L.L. Sonnhammer and J.C. Wootton, "Integrated Graphical Analysis of Protein Sequence Features Predicted from Sequence Composition," Proteins: Structure, Function, and Genetics, vol. 45, pp. 262-273, 2001.
32. R.S. Stephens, S. Kalman, C. Lammel, J. Fan, R. Marathe, L. Aravind, W. Mitchell, L. Olinger, R.L. Tatusov, Q. Zhao, E.V. Koonin, and R.W. Davis, "Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia Trachomatis," Science, vol. 282, no. 5389, pp. 754-759, Oct. 1998.
33. H. Tettelin, N.J. Saunders, J. Heidelberg, A.C. Jeffries, K.E. Nelson, J.A. Eisen, K.A. Ketchum, D.W. Hood, J.F. Peden, R.J. Dodson, W.C. Nelson, M.L. Gwinn, R. DeBoy, J.D. Peterson, E.K. Hickey, D.H. Haft, S.L. Salzberg, O. White, R.D. Fleischmann, B.A. Dougherty, T. Mason, A. Ciecko, D.S. Parksey, E. Blair, H. Cittone, E.B. Clark, M.D. Cotton, T.R. Utterback, H. Khouri, H. Qin, J. Vamathevan, J. Gill, J.V. Scarlato, V. Masignani, M. Pizza, G. Grandi, L. Sun, H.O. Smith, C.M. Fraser, E.R. Moxon, R. Rappuoli, and J.C. Venter, "Complete Genome Sequence of N. Meningitidis Serogroup B Strain MC58," Science, vol. 287, no. 5459, pp. 1809-1915, Mar. 2000.
34. J.F. Tomb et al., "The Complete Genome Sequence of the Gastric Pathogen Helicobacter Pylori," Nature, vol. 388, no. 6642, pp. 539-547, Aug. 1997.
35. D. Voorhies, "Space-Filling Curves and a Measure of Coherence," Graphics Gems, pp. 26-30, Academic Press, 1991.
36. M. Waterman, Introduction to Computational Biology: Maps, Sequences and Genomes. New York: Chapman & Hall, 1995.
37. N. Wirth, Algorithms + Data Structures = Programs. Prentice Hall, 1976.
38. D. Wu, J. Roberge, D.J. Cork, B.G. Nguyen, and T. Grace, "Computer Visualization of Long Genomic Sequences," Proc. IEEE Visualization '93, pp. 308-315, Oct. 1993.