BARD: a visualization tool for biological sequence analysis

Authors:
Rhazes Spell;Rachael Brady;Fred Dietrich
Affiliations:
Duke University, Department of Biomedical Engineering;Duke University, Pratt School of Engineering;Duke University Medical Center, Department of Molecular Genetics and Microbiology
Venue:
INFOVIS'03 Proceedings of the Ninth annual IEEE conference on Information visualization
Year:
2003

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Abstract

We present BARD (biological arc diagrams), a visualization tool for biological sequence analysis. The development of BARD began with the application of Wattenberg's arc diagrams [Wattenberg 2002] to results from sequence analysis programs, such as BLAST [Altschul et al. 1990]. In this paper, we extend the initial arc diagram concept in two ways: 1) by separating the visualization method from the underlying matching algorithm and 2) by expanding the types of matches to include inexact matches, complemented palindrome matches, and inter-sequence matches. BARD renders each type of match distinctly, resulting in a powerful tool to quickly understand sequence similarities and differences. We illustrate the power of BARD by applying the technique to a comparative sequence analysis of the human pathogenic fungi Cryptococcus neoformans.