Linking to GenomeView

You can directly link to GenomeView using a URL and specify four parameters. This example shows the parameters:

http://synteny.cnr.berkeley.edu/CoGe/GenomeView.pl?z=5&x=200000&dsgid=3068&chr=scaffold_3

• x= Specifies the basepair coordinate on which to center GenomeView.
• chr= The chromosome. This must be correct for the genome. For example, "scaffold_3" or "3" or "III".
• dsgid= CoGe's database id for the genome.
• z= The zoom level. There are 20 zoom levels (0-19). 0 is most zoomed out and 19 is most zoomed in. Zoom level 12 gives a resolution of 1 basepair per pixel, zoom level 0 is 4096 basepairs per pixel, and zoom level 19 is 64 pixels per basepair (0.015625 basepairs per pixel).
• sl=1 Show the legend. The legend is not shown by default, and requires the user to click a button named "show legend".

To find the dsgid and valid chromosome names for a genome, use OrganismView. Search for an organism and genome of interest. When you find it, the dsgid is listed next to the genome name in the list of genomes in the selectable menu under the header "Genomes:". Valid chromosomes names for a genome are found when the genome of interest is selected. The chromosomes are listed in a drop down menu under the header "Chromosomes:". Sometimes a genome is comprised of multiple datasets, and each dataset contains some subset of the chromosomes (usually just one). You may have to search through different datasets to make sure you find all the valid chromosome names.