BARD: A visualization tool for biological sequence analysis

Proceedings - IEEE Symposium on Information Visualization, INFO VIS

Volumn , Issue , 2003, Pages 219-226

  Spell, Rhazes ^a   Dietrich, Fred ^a   Brady, Rachael ^b  

^a Duke University   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Arc diagram; BARD; Comparative genomics; Sequence analysis; Visualization

Indexed keywords

APPLICATION PROGRAMS; FLOW VISUALIZATION; FUNGI; INFORMATION SYSTEMS;

ARC DIAGRAM; BARD; BIOLOGICAL SEQUENCE ANALYSIS; COMPARATIVE GENOMICS; COMPARATIVE SEQUENCE ANALYSIS; CRYPTOCOCCUS NEOFORMANS; SEQUENCE ANALYSIS; VISUALIZATION METHOD;

VISUALIZATION;

EID: 16244404503     PISSN: 1522404X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/infvis.2003.1249029     Document Type: Conference Paper

References (16)

1. Altschul, S. F., Gish, W., Miller, W., Meyers, E. W., and Lipman, D. J. 1990. Basic local alignment search tool. J Mol Biol 215, 3, 403-410.
2. Bederson, B., Meyer, J., and Good, L. 2000. Jazz: An extensible zoomable user interface graphics toolkit in Java. In ACM Symposium on User Interface Software and Technology, vol. 2(2), 171-180.
3. Casadevall, C., and Perfect, J. R. 1998. Cryptococcus neoformans. ASM Press.
4. Dubchak, I., Brudno, M., Pachter, L. S., Loots, G. G., Mayor, C., Rubin, E. M., and Frazer, K. A. 2000. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Research 10, 1304-1306.
5. Durbin, R., Eddy, S., Krough, A., and Mitchison, G. 2001. Biological Sequence Analysis. Cambridge University Press.
6. European Moleculare Biology Open Software Suite, 2003. [online] http://www.sanger.ac.uk/software/formats/gff/.
7. Gibbs, A. J., and McIntyre, G. A. 1970. The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. Eur J Biochem 16, 1, 1-11.
8. Heitman, J., Casadevall, C., Lodge, J., and Perfect, J. R. 1999. The Cryptococcus neoformans genomce sequencing project. Mycopathologia 148, 1-7.
9. Hull, C. M., Davidson, R. C., and Heitman, J. 2002. Cell identity and sexual development in Cryptococcus neoformans are controlled by the mating-type-specific homeodomain protein sxi1alpha. Genes Dev 16, 23, 3046-3060.
10. Kent, W. J., and Zahler, A. M. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Research 10, 8, 1115-1125.
11. Kwon-Chung, K. J., Edman, J. C., and Wickes, B. L. 1992. Genetic association of mating types and virulence in Cryptococcus neoformans. Infect. Immun. 60, 602-605.
12. Mayor, C., Brudno, M., Schwartz, J., Poliakov, A., Rubin, E. M., Frazer, K. A., Pachter, L. S., and Dubchak, I. 2000. Vista : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16, 11, 1046-1047.
13. Mitchell, T., and Perfect, J. R. 1995. Cryptococcosis in the era of aids-100 years after the discovery of Cryptococcus neoformans. Clin. Microbiol. Rev. 8, 515-548.
14. Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W. 2000. Pipmaker-a web server for aligning two genomic DNA sequences. Genome Research 10, 4, 577-585.
15. The Wellcome Trust Sanger Institute, 2003. http://www.sanger.ac.uk/ software/formats/gff/.online.
16. Wattenberg, M. 2002. Arc diagrams: Visualizing structure in strings. In IEEE Symposium on Information Visualization, ACM, 110-116.