Why Stacking Does Not Work in GBrowse?

The illustration below shows why stacking contigs does not work in GBrowse. This example is from an early compile of soybean data for GBrowse. All of the loci for the location are at the top; all of the clones are in the middle; and, all of the contigs are at the bottom. The problem is that the related loci/clones/contigs are not grouped together. Comparing with the Boats on a Lake, this would be like stacking all of the boat hulls together, putting all of the decks on the top hull, and then putting all of the the masts on the top deck. Our solution to this problem with our soybean data in GBrowse was to spread out the contigs with their associated features, like spreading out the "boats on a lake," so that one can graphically see what features go together.

The ideal solution, if GBrowse could do it, would be to first display a single contig with all of its clones and loci. Then, below that, display the next contig with all of its clones and loci. Then, continue in this manner until all of the contigs, and their associated features, are displayed.

Deepak
http://soybeangenome.siu.edu
Last update: July 31,2005.