GenomePixelizer was designed to help in visualizing the
relationships between duplicated genes in genome(s) and
to follow relationships between members of gene clusters.
GenomePixelizer may be useful in the detection of
duplication events in genomes, tracking the "footprints" of
evolution, as well as displaying the genetic maps and
other aspects of comparative genetics.
GenomePixelizer may be considered a drawing tool that generates
custom images of genomes out of the given set of genes.
Each element on the picture has a physical address defined by
coordinates (pixels), hence the name "GenomePixelizer".
We developed and are using GenomePixelizer to analyze the evolution of NBS-LRR encoding
genes in Arabidopsis relative to other genome duplication events.
Features of GenomePixelizer:
1. Written in Tcl/Tk and works on any computer platform (Unix/Linux, Windows, Mac)
that support the Tcl/Tk toolkit.
2. GenomePixelizer does not need to be compiled; it works like Perl or Python scripts,
using the Tcl/Tk language interpreter which can be downloaded for free at
3. GenomePixelizer allows the display of desired features through the whole genome simultaneously.
Generated images should fit into the user's computer monitor without scrolling.
For larger genomes, it is possible to generate bigger images with a build-in scroll-bar.
4. Simple and flexible input file may be set up, edited and modified using any
spreadsheet editor (e.g. MS Excel or StarOffice). Researcher can easily manipulate
the set of genes of interest, add new sets, change or remove old ones and re-run
program on a fly.
5. Zoom in functionality, cluster viewing, minimal modification in the input file and some
simple re-calculations allow the viewing of regions of high gene density in greater detail.
6. Regions with high gene density can be drawn using automatic or manual correction.
Manual correction may produce nicer images; however with large set of genes it
7. GenomePixelizer allows the viewing of relationships between different sets
of genes based on a distance matrix file.
8. The source of sequences is not restricted to a single organism and it is possible
to view relationships between different genomes.
9. GenomePixelizer can be used to generate images of genetic maps with a given set of genetic
markers. Instead of megabases, the size of chromosomes should be indicated
10. Generated images can be captured by any screenshot program and incorporated into
Web pages. You can also save the generated image as a PostScript file.
11. GenomePixelizer can generate HTML ImageMap tags. This feature can be used to create "clickable"
images for Web pages or online presentations.
12. The source code is freely available and minimal code modifications can
add new features to the program.
GenomePixelizer is under the GNU General Public License
Copyright © 2001 University of California at Davis