BARD: a visualization tool for biological sequence analysis

摘要

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 (Atschul 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.