PQuad: Visualization of predicted peptides and proteins

IEEE Visualization 2004 - Proceedings, VIS 2004

Volumn , Issue , 2004, Pages 473-480

  Havre, Susan L ^a   Singhal, Mudita ^a   Payne, Deborah A ^a   Webb Robertson, Bobbie Jo M ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Context; Difference visualization; Differential proteomics; Metaphor; Proteomics; Visualization

Indexed keywords

DIFFERENCE VISUALIZATION; DIFFERENTIAL PROTEOMICS; METAPHORS; PROTEOMICS;

COMPUTER GRAPHICS; DNA; ENZYMES; FLOW VISUALIZATION; GENES; MASS SPECTROMETRY; PROTEINS;

POLYPEPTIDES;

EID: 17044429698     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (24)

1. D. W. Speicher, "Proteomics: an infinite problem with infinite potential," The Scientist, vol. 16, pp. 12, 2002.
2. J. R. Yates, J. K. Eng, A. L. McCormack, and D. Schieltz, "Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database," Analytical Chemistry, vol. 67, pp. 1426-1436, 1995.
3. M. Mann and M. Wilm, "Error-tolerant identification of peptides in sequence databases by peptide sequence tags," Analytical Chemistry, vol. 66, pp. 4390-4399, 1994.
4. J. K. Eng, A. L. McCormack, and J. R. I. Yates, "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database," Journal of the American Society for Mass Spectrometry, vol. 5, pp. 876-989, 1994.
5. S. K. Card, J. D. Mackinlay, and B. Shneiderman, Readings in Information Visualization: Using Vision to Think. San Francisco: Morgan Kaufmann Publishers, Inc, 1999.
6. GeneSpring, "Silicon Genetics," vol. http://www. silicongenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf. Redwood City, CA.
7. OmniViz, vol. http://www.omniviz.com/. Maynard, MA.
8. Spotfire, Somerville, MA.
9. TIGR, "The Institute for Genomic Research," http://www.tigr.org/.
10. L. S. Heath and N. Ramakrishnan, "The Emerging Landscape of Bioinformatics Software Systems," IEEE Computer, pp. 41-45, 2002.
11. J. D. Jaffe, H. C. Berg, and G. M. Church, "Proteogenomic mapping as a complementary method to perform genome annotation," Proteomics, vol. 2004, pp. 59-77, 2004.
12. K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice, M. A. Rajandream, and B. Barrell, "Artemis: sequence visualization and annotation," Bioinformatics, vol. 16, pp. 944-5, 2000.
13. EMBL-EBI, "European Bioinformatics Institute," http://www.ebi.ac.uk/embl/.
14. GenBank, "GenBank: NIH genetic sequence database," www.ncbi.nlm.nih.gov/.
15. T.-M. Rhyne, J. P. Lee, D. Carr, G. Grinstein, J. Kinney, and J. Saffer, "Visualization Viewpoints: The Next Frontier for Bio- and Cheminformatics Visualization," IEEE Computer Graphics and Applications, vol. 2002, pp. 6-11, 2002.
16. D. F. Jerding and J. T. Stasko, "The Information Mural: A Technique for Displaying and Navigating Large Information Spaces," In Proceedings of IEEE Symposium on Information Visualization 1995, Atlanta, Georgia, 1995.
17. C. Plaisant, D. Carr, and B. Shneiderman, "Image-Browser Taxonomy and Guidelines for Designers," IEEE Software, vol. 12, pp. 21-32, 1995.
18. T.-M. Rhyne, "Evolving Visual Metaphors and Dynamic Tools for Bioinformatics Visualization," In Proceedings of IEEE Visualization Conference 2002, Boston, Massachusetts, 2002.
19. J. C. Avise, "Evolving Genomic Metaphors: A New Look at the Language of DNA," Science, vol. 294, pp. 86-87, 2001.
20. P. C. Wong, K. K. Wong, H. Foote, and J. J. Thomas, "Global visualization and alignments of whole bacterial genomes," IEEE Transactions on Visualization and Computer Graphics, vol. 9, pp. 361-377, 2003.
21. KEGG, "Kyoto Encyclopedia of Genes and Genomes."
22. GO, "Gene Ontology."
23. C. G. Healey and J. T. Enns, "Large datasets at a Glance: Combining Textures and Colors in Scientific Visualization," IEEE Transactions on Visualization and Computer Graphics, vol. 5, pp. 145-167, 1999.
24. S. Havre, M. Singhal, B. Gopalan, D. Payne, K. Klicker, G. Kiebel, K. Auberry, E. Stephan, B.-J. Webb-Robertson, and D. Gracio, "Integrating Evolving Tools for Proteomics Research," In Proceedings of International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, NV, 2004.