Genomic dot plot software

Alexander Kozik akozik at atgc.org
Sun Mar 2 14:46:33 EST 2003


We are pleased to announce the GenomePixelizer 2D plotter:
http://www.atgc.org/GenoPix_2D_Plotter/
and DiagHunter:
http://www.tc.umn.edu/~cann0010/Software.html

The two programs are designed to study segmental
duplications within a given genome, or synteny between
different genomes. Both programs come with example data
for the entire Arabidopsis thaliana genome.

GenomePixelizer 2D plotter generates genomic dot plots,
using an interactive "canvas" that allows different groups of
genes (for example, gene families) to be colored, and genes
to be searched and highlighted. The program can also
produce PostScript files of any size. GenomePixelizer 2D
plotter is implemented in Tcl/Tk and works on any
computer system that supports the Tcl/Tk interpreter
(available at  http://tcl.activestate.com/  ).

DiagHunter identifies diagonal features (syntenic regions)
in a genomic dot plot, and displays these in dot plot images
in PNG file format. DiagHunter also produces text files
with detailed information about detected diagonals.
DiagHunter is implemented in Perl. The GD graphic libraries
are required to generate images.

Comments and feedback are very welcome.

Alexander Kozik ( akozik at atgc.org )
Steven Cannon ( cann0010 at tc.umn.edu )
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