GenomePixelizer 2D Plotter Program Download:
Download current version GenoPix_2D_Plotter_July_23_2003.tar.gz
Download Tcl/Tk toolkit from tcl.activestate.com
Supplemental data: Arabidopsis predicted protein sequences
BLAST parser: tcl_blast_parser_123
GenBank parser: GenBank_parser.py
Arabidopsis Genome dataset corresponding to recent annotation (TIGR Release Version 4.0, May 2003)
GenoPix2D and DiagHunter reference: Genome Biology 2003, 4:R68
NOTE ABOUT CHROMOSOME NUMBERING:
GenoPix_2D_Plotter reads and understands chromosome IDs as strings (not as integers). If your dataset has
more than 9 (nine) chromosomes you should label them as 01 02 03 ... 08 09 10 11 ... and so on. Program
does not work properly sometime if chromosomes are labeled by different way.
QUICK START
1. Download and uncompress current version of GenoPix_2D_Plotter.
2. if Tcl/Tk is not installed on your computer, download and install interpreter
from tcl.activestate.com
3. Run genoPix2D_July_23_2003.tcl from command shell or by mouse click on Windows.
4. Click "Load Data".
5. Click "Load Annotation".
6. Change value of "Chr Y dir" from 1 to 3.
7. Click "Plot Canvas" (chromosome 1 against chromosome 3 should be plotted on canvas, it may take several minutes).
8. Open "Node Painter". Click on "paint" of group 1 (all resistance-like genes will be painted in red).
Click on "paint" of group 2 (all cytochrome P450 genes will be painted in green).
9. Click on any element (dot) on canvas. In Annotation window info about selected genes should be displayed.
In Gene IDs window gene IDs and corresponding coordinates should be displayed.
10. On main window change values "Start" - "End"
for chromosome 1: "Start": 16.9 "End": 21.0
for chromosome 3: "Start": 3.6 "End": 7.9
then click "Plot Canvas" again. Canvas with selected genome regions should be generated.
11. Click on "paint" of "diagonal group" on "Node Painter" window. Segmental duplications detected by
Steven Cannon's DiagHunter will be painted in purple.
12. Click on "Color Reset" on "Node Painter" window. You get back to gray-scale mode
13. On the bottom of the Annotation window type in keyword "kinase" (green entry field) and press "Enter" key.
All genes with keyword "kinase" in description line from annotation will be painted in blue.
14. For detailed program description click on "Help"
previous version GenoPix_2D_Plotter_June_23_2003.tar.gz