DCJVis: visualization of genome rearrangements using DCJ operations

TL;DR

DCJVis is a novel visualization tool that graphically represents genome rearrangements using DCJ operations, aiding biologists in understanding complex genome transformations through circular layout diagrams.

Contribution

This paper introduces DCJVis, the first visualization software for DCJ operations, facilitating the interpretation of genome rearrangements with an intuitive circular layout.

Findings

Successfully visualizes DCJ operations between genomes.

Demonstrates functionality with yeast genomes.

Helps biologists understand genome rearrangements.

Abstract

The {\em double-cut-and-join} (DCJ) operation, introduced by Yancopoulos \emph{et al.}, allows minimum edit distance to be computed by modeling all possible classical rearrangement operations, such as inversions, fusions, fissions, translocations, and transpositions, in linear-time between two genomes. However, there is lack of visualization tool that can effectively present DCJ operations that will help biologists to use DCJ operation. In this paper, a new 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 on the source genome for the DCJ operation. Our program is the first visualization tool for DCJ operations using circular layout. Specifically, the genomes of \textit{Saccharomyces cerevisiae} and \textit{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.