All annotation is displayed in the space above the gene and below the PAR graph as shown by the circled areas below:
Each type of annotation is displayed in a unique color and grouped together on the same annotation "track". For example, in the Transcript View of the image above, all the domains are displayed in purple on a track directly above the gene. Immediately above the domain track is the SNP track which shows all of the SNPs in yellow.
The annotation displayed in the Transcript View is specific to the coding portion of the gene such as functional domains and secondary structures. The annotation displayed in the Genomic View is not coding-specific such as SNPs.
Open the Annotation Options window by clicking on "Annotation Options..." from the "Options" menu. The following window will appear:
To modify options for a specific type of annotation, select the type from the Annotation Type drop-down list. By editing the Display Name, you will modify what displays on the annotation track when you hover your mouse over the annotation.
See the section on Display Modes for understanding the Display Mode drop-down options.
The rest of the options modify how the PAR algorithm handles the annotation. Visit Prioritized Screening for more details.
Each type of annotation has three different display modes: Full, Small, and Hidden.
| Description | Example |
| Full: Each unique annotation is displayed as its own distinct rectangle lined up appropriately above the gene. If multiple instances of the same type of annotation overlap, then the annotation track will grow taller to accommodate the necessary space to display each instance of the annotation. |  |
| Small: The annotation track is condensed to the height of a single layer. If multiple instances of the same type of annotation overlap, then the overlapping portion will be darker than the non-overlapping portion to indicate the presence of the overlap. |  |
| Hidden: As its name suggests, the annotation will not be visible at all. |  |
There are two ways to change the display mode for a type of annotation:
Details about annotation may be retrieved from the "Get Details..." right-click menu. Select one or more instances of annotation and then right-click (or Ctrl+click) one of the instances that has been selected. You will see a menu appear as shown below:
Click on "Get Details..." and you will see a window appear similar to this:
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This window contains all of the details about the selected annotation. If multiple instances were selected, each will appear in its own tab which may be selected at the top of the window. This information may be printed or saved locally to a file. |