A Tool for Visualizing Multiple Genome Comparisons
Asem Othman and Mohamed Ibrahim Abouelhoda
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.
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
VisCHAINER is written in Java and it was tested under the following
- Plotting all or some selected projections of the multi-dimensional chains.
- Displaying the chains computed w.r.t. the forward and/or reverse
- Zooming in/out.
- 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.
Please see the user manual and tutorial for details.
- Linux (Redhat, SuSe, Debian) for Intel and AMD architectures
- Solaris for the SUN/Sparc architecture
- Windows XP
VisCHAINER was developed by
Asem Othman, Dept. of Biomedical Engineering, Cairo University, Egypt,
Mohamed Ibrahim Abouelhoda,
Dept. of Theoretical Bioinformatics, University of Ulm,
VisCHAINER is free for
academic research, educational, and demonstration purposes.