VisCHAINER
A Tool for Visualizing Multiple Genome Comparisons

(Beta Version)

Asem Othman and Mohamed Ibrahim Abouelhoda

2008

This is the beta version of the program VisCHAINER, the interactive visualization component of the software system CoCoNUT. In the user manual and tutorial, we explain how to use VisCHAINER. Here we outline the most important features of the program.

Features of VisCHAINER

The current version of VisCHAINER plots the chains output by the program CHAINER . Each chain corresponds to a region of similarity among two or multiple genomes. Because these chains are multi-dimensional VisCHAINER displays projections in 2D plots. The user of VisCHAINER has the following options:

1. Plotting all or some selected projections of the multi-dimensional chains.
2. Displaying the chains computed w.r.t. the forward and/or reverse complementary strands.
3. Zooming in/out.
4. Selecting chains within a region and displaying the associated features (nucleotide sequences and score). The selected results can be stored in separate files so that other programs can be called to process them.

Technology and Platforms

VisCHAINER is written in Java and it was tested under the following platforms:

• Linux (Redhat, SuSe, Debian) for Intel and AMD architectures
• Solaris for the SUN/Sparc architecture
• Windows XP

Formats and Usage

Please see the user manual and tutorial for details.

Developers

VisCHAINER was developed by

Asem Othman, Dept. of Biomedical Engineering, Cairo University, Egypt, and

Mohamed Ibrahim Abouelhoda, Dept. of Theoretical Bioinformatics, University of Ulm, Germany.

Availability

VisCHAINER is free for academic research, educational, and demonstration purposes.
Download VisCHAINER: Download Link