Visualization of genome rearrangements using DCJ operations

The powerful double-cut-and-join (DCJ) operation, introduced by Yancopoulos et al. [18], supports all classical genome rearrangement operations. This allows minimum edit distance to be computed by modeling all possible classical rearrangement operations. However, there is a lack of visualization tools that can effectively present DCJ operations that will help biologists to use DCJ operations. In this paper, a novel visualization program is introduced, DCJVis, to create a diagram of each DCJ operation necessary to transform between the genomes of two distinct organisms by describing a possible sequence of genome graphs based on the selected gene adjacency for the DCJ operation. Our program is the first visualization tool for DCJ operations using circular layout, consistent colors, supports FASTA input. Specifically, the genomes of Saccharomyces cerevisiae and Candida albicans are used to demonstrate the functionality of this program and provide an example of the type of problem this program can solve for biologists.

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