Placing the mouse arrow over a gene feature on a data track highlights the gene and displays a thumbnail gene map providing a brief summary of the feature including the data track name, a systematic name, and a small map of the feature (left figure below). In order for the miniature graphic to be displayed the checkbox for Show Annotation Preview (Tools>Settings>Balloon) must be checked (see Settings).

Track Right-Click Menu

If you right click on a data track, the right-click menu is displayed (right figure below).

Gene Information on Map

Track Contexual Menu

The options in this menu are described below.

Link Tracks

Select this option to link tracks on different plates.

Link Track Menu

Show/Hide Tracks

Provides a checkbox menu for selecting the data tracks to be displayed.

Map Show/Hide Track Menu

Hide this Track

Indicates the track currently selected and enables you to hide it.

Find Synteny

Provides a listing of species and their respective chromosomes with syntenic relationships. Please see Comparing Maps for more information.

Invert Plate

This will reverse the orientation of the entire plate and all tracks, so that the first nucleotide is now displayed at the bottom of the plate rather than the top.

Close Plate

Closes the entire plate.

Pin Plate Down

Pins the plate down.

Export Gene Region

See Export Track Window for more information.

Export Gene Region (New)

See Export Track Window for more information.

Export track

See Export Track Window for more information.

Export track (New)

See Export Track Window for more information.

Map Properties

This selection opens a window to display information about all data tracks available on the plate whether they are displayed or not (see the figure below). The Map Set Details button at the top right of the window will open up another window showing various details about the Map itself, such as the source of the data.

Map Properties window (left) and Map Set Details window (right)

Track Properties

Similar to Map properties but for the specific track selected when the right-click menu was selected is highlighted in the Tracks panel.

Vertical Track Display Information

There are several additional features in the vertical track display. In the figure below, several of the genes have vertical gray bars on the black centerline of the data track adjacent to genes. This indicates that the gene has several gene model predictions, although only one is shown. In the figure on the right, the gene is highlighted and the screen tip shows three potential models for the gene rather than just a single model. Only genes with the gray bar will have multiple models available based on the current data in Persephone.

Tip

You can select how many models to show in Settings > Balloon > Maximum Annotations. See Settings for more information.

 

Map - Vertical Track Information

Map - Vertical Track Information - Selected Gene

The annotation information available for a gene (physical maps only) can be displayed by clicking on a gene feature as shown below. The selected gene, shown below, will be highlighted when you click on it.

Track Annotation Details Displayed

Creating New Tracks

If a genetic map has a large number of items, you can select a subset of markers and display them as a separate track with a new name. To do this, click the genetic map with the right mouse button and select Create new track from the menu as shown below.

Marker data track context menu

A Genetic Map Filter window will be displayed (see the figure below). Marker names, separated by commas, can be typed into the entry field at the top of the page. If you click the ellipsis button, a window will appear, which will enable you to open a file of names or alternatively type in a list of marker names by hand, one per line, or on a single line separated by commas. The downward-pointing arrowhead shows previous marker name entries. The downward-pointing arrowhead shows previous marker name entries. The form also contains entry fields for Marker Type, Source Organism, and Source (of data).

Genetic Map Filter

You can further define the marker list by entering Marker Qualifiers or Mapping Qualifiers. The Qualifiers button for each will bring up a new Qualifiers window to specify Qualifier Value pairs.

Qualifiers-Values window

And the following shows the window to select qualifier values.

SNP offset values

Clicking the Search button will indicate the number of markers found. Finally, you need to enter a name into the Track Name field at the bottom of the window. Click Create and a new marker track with the track name you entered will appear next to the previous one in the same plate and populated with the filtered data.

Custom Track Example