GenomePixelizer - Genome Visualization Tool



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GenomePixelizer Description:

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 www.scriptics.com or tcl.activestate.com.

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 takes time.

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 in centiMorgans.

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




Description
Screenshots
Examples
Manual
Download
Feedback
Authors


email: Alexander Kozik

Last modified, July 03 2002