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Visualize in Genomica

Visualizing the results in Genomica


Our predictions can be viewed and browsed through in the genome browser of Genomica, a statistical analysis and visualization tool that we developed. The predictions include the predicted expression pattern for each cis-regulatory sequence module across the entire antero-posterior axis of the embryo, and the distribution of factor occupancies along the antereo-posterior axis as computed by our model. Many of the figures in the paper were generated directly by such visualizations in Genomica.

NOTE: GENOMICA IS FREELY AVAILABLE FOR ACADEMIC USE ONLY

Instructions:


  1. Install Genomica.
  2. Download expression prediction.
  3. Browse the expression predictions. Open the file (model.gxp) and scan through each of the sequence modules by clicking on the "T" button in the toolbar in Genomica. In order to get an enlarged view of the modules, click on the "set selection properties" button in the table view (left panel, bottom right button) and set the "extend view in each direction by" under the "Tracks" tab to zero.
    Refer to the Genomica website for detailed tutorials on how to use the tool in general and the genomie browser in particular. .