Visualization of information with an established order

Image analysis – Applications – Biomedical applications

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

Reexamination Certificate

active

10120132

ABSTRACT:
Among the embodiments of the present invention is a system including one or more processors operable to access data representative of a biopolymer sequence of monomer units. The one or more processors are further operable to establish a pattern corresponding to at least one fractal curve and generate one or more output signals corresponding to a number of image elements each representative of one of the monomer units. Also included is a display device responsive to the one or more output signals to visualize the biopolymer sequence by displaying the image elements in accordance with the pattern.

REFERENCES:
patent: 4805016 (1989-02-01), Kato
patent: 5228123 (1993-07-01), Heckel
patent: 5416848 (1995-05-01), Young
patent: 5473736 (1995-12-01), Young
patent: 5583973 (1996-12-01), DeLisi et al.
patent: 5891632 (1999-04-01), Imai
patent: 6058211 (2000-05-01), Bormans et al.
patent: 6151595 (2000-11-01), Pirolli et al.
patent: 6203977 (2001-03-01), Ward et al.
patent: 6263287 (2001-07-01), Zheng et al.
patent: 2001/0047376 (2001-11-01), Shaw
Hao, Bai-lin, “Fracals from genomes—exact solutions of a biology-inspired problem”, Institue of Theoretical Physics, People's Republic of China, Feb. 1, 2000.
Chi at el, “A Novel Visualization Method for biological Sequences Similarity”, University of Minnesota, Nov. 30, 1999.
Moon at el, “Analysis of the Clustering Properties of the Hilbert Space-Filling Curve”, IEEE Transactions on Knowledge and Data Engineering, vol. 13, No. 1, Jan./Feb. 2001.
Wong et al. “Global Visualization and Alignments of Whole Bacterial Genomes”, Jul.-Sep. 2003, IEEE Transactions on Visualization and Computer Graphics, vol. 3, No. 3, pp. 361-377.
D.A. Keim, “Designing Pixel-Oriented Visualization Techniques: Theory and Applications, ” IEEE Trans. Visualization and Computer Graphics, vol. 6, No. 1, Jan.-Mar. 2000.
Lantin et al. “Supporting detail-in-context for the DNA representation, H-curves”, Proceedings of the conference on Visualization '98, pp. 443-446.
Keim, Daniel “Information Visualizatin and Visual Data Mining”, IEEE Transactions on Visualization and Computer Graphics, vol. 8, No. 1, Jan.-Mar. 2002.
Genome Image; htt://ivpr.cs.uml.edu/gallery/images/large/genome/Genome2.jpg; as least as early as Mar. 5, 2002.
Genome Image; htt://ivpr.cs.uml.edu/gallery/images/large/genome/Genome1.jpg; as least as early as Mar. 5, 2002.
Ashish Marnania, Georges Grinstein and Kenneth A. Marx,GENVIS: A Sequence Visualization Technique for Genomic DNA, University of Massachusetts at Lowell, SPIE vol. 2656, p. 189, (Date Unknown).
M.L. Lantin and M.S.T. Carpendale, “Supporting Detail-in-Context for the DNA Representation, H-Curves,” Simon Fraser University, (Date Unknown).
Dean F. Jerding and John T. Stasko, “The Information Mural: A Technique for Displaying and Navigating Large Information Spaces”, Georgia Institute of Technology, Atlanta, GA., 1997.
Dean F. Jerding and John T. Stasko, “The Information Mural”, Georgia Institute of Technology, Atlanta, GA., Mar. 1996.
H. Joel Jeffrey, “Chaos game representation of gene structure”, Northern Illinois, University, DeKalb, Illinois, Nucleic Acids Research, vol. 18, No. 8, p. 2163, Mar. 20, 1990.
V.V. Solvovyev, S.V. Korolev, and H. A. Lim, “A New Approach for the Classification of Functional Regions of DNA Sequences Based On Fractal Representations”, Int'l J. Genomic Res. 1:108-127, Russian Academy of Sciences & Florida State University, Jun. 3, 1991.
Ed Huai-hsin Chi, Phillip Barry, Elizabeth Shoop, John V. Carlis, Ernest Retzel, and John Riedl, “Visualization of Biological Sequence Similarity Search Results,” University of Minnesota, 1995.
Ed Huai-hsin Chi, Phillip Barry, Elizabeth Shoop, John V. Carlis, Ernest Retzel, and John Riedl, “Flexible Information Visualization of Multivariate Data from Biological Sequence Similarity Searches”, University of Minnesota, 1996.
Peter Ti{umlaut over (n)}o and Georg Dorffiner,Constructing finite-context sources from fractal representations of symbolic sequences, Austrian Research Institute for Artificial Intelligence, 1998.
Guillermo Abramson, Hilda A. Cerdeira, and Carlo Bruschi, “Fractal properties of DNA walks”, Int'l. Centre for Theoretical Physics and Int'l. Centre for Genetic Engineering and Biotechnology, Mar. 26, 1998.
Bai-lin Hao, H.C. Lee, and Shu-yu Zhang, “Fractals related to long DNA sequences and complete genomes”, Chaos, Solitons and Fractals, Elsevier Science Ltd., 2000.
Peter Ti{umlaut over (n)}o “Spatial Representation of Symbolic Sequences through Iterative Function Systems”, Austrian Research Institute for Artificial Intelligence, Austria, 1998.
Ed Huai-hsin Chi, Phillip Barry, Elizabeth Shoop, and John Riedl, “A Novel Visualization Method for Biological Sequences Similarity”, University of Minnesota, Nov. 30, 1999.
Bai-lin Hao, “Fractals from genomes—exact solutions of a biology-inspired problem”, Institute of Theoretical Physics, People's Republic of China, Feb. 1, 2000.
David B. Searls, “Visualizing the Genome”, SmithKline Beecham Pharmaceuticals, (At least as early as Dec. 17, 2001).
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, T.J. Trust, “Genomic Sequence Comparison of Two Unrelated Isolates of the Human Gastric PathogenHelicobacter pylori,” Nature, vol. 397, No. 6715, pp. 176-180, Jan. 1999.
S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman, “Basic local alignment search tool,”Journal of Molecular Biology, vol. 215, No. 3, pp. 403-410, 1990.
A.R. Butz, “Alternative Algorithm for Hilbert's Space-Filling Curve,”IEEE Transactions on Computers, vol. C-20, No. 4, pp. 424-426, Apr. 1971 (copy unavailable).
S.K. Card, J.D. Mackinlay, and B. Shneiderman,Readings in Information Visualization—Using Vising To Think, Morgan Kaufmann, 1999 (copy unavailable).
E.H. Chi, P. Barry, E. Shoop, J.V. Carlis, E. Retzel, and J. Riedl, “Visualization of Biological Sequences Similarity Search Results,”Proceedings IEEE Visualization 95, pp. 44-51, IEEE Computer Society Press, Los Alamitos, CA, Oct. 1995.
E.H. Chi, J. Riedl, E. Shoop, J.V. Cartis, E. Retzel, and P. Barry, “Flexible Information Visualization of Multivariate Data from Biological Sequence Similarity Searches,”Proceedings IEEE Visualization 96, pp. 133-140, ACM Press, NY, NY, Oct. 1996.
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.
L. Florca, 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.
A.J. Gibbs and G.A. McIntyre, “The Diagram, A Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences,”European Journal of Biochemistry, vol. 16, pp. 1-11, 1970 (copy unavailable).
R.C. Gonzalez and R.E. Woods,Digital Image Processing, Addison Wesley, 1992 (copy unavailable).
E. Hamori and J. Ruskin, “H Curves, A Novel Method of Representation of Nucleotide Series Especially Suited for Long DNA Sequences,”The Journal of Biological Chemistry, vol. 258, No. 2, pp. 1318-1327, Jul. 1983.
http://www.stat.duke.edu/courses/sta1xx/Data—sets/data—sets.html.
http://www.gcg.com/products/macvector.html.
http://www.ncbi.nlm.nih.gov.
http://www.tigr.org/tdb/mdb/mdb.html.
D. Jerding and J. Stasko, “The Information Mural: A Technique for Displaying and Navigating Large Information Sp

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Visualization of information with an established order does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Visualization of information with an established order, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Visualization of information with an established order will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3827438

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.