This section describes how to display map details with the right-click menu.

Tip

Please refer to Navigating Persephone to see how maps can be displayed, moved around, and scaled.

Map Properties

Right click on a plate to display a right-click menu as shown below.

Plate context menu

One of the menu item selections is Map Properties, which will show general map details as well as the track properties. Map properties can also be selected from a data track right-click menu. Clicking on the Map Set Details button will bring up a window with detailed Map Set properties (shown to the right below).

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

Genetic Maps

Genetic maps (linkage groups) show marker positions in centiMorgans (cM).

Fragment of Genetic map

The marker labels on the genetic map are clickable. If you click on the marker name, it will display a Marker Details window (see Marker Details) including the marker sequences, positions on different maps, associated sequences, and other qualifiers.

A marker can have several names but only one, designated as the primary, is shown on the map. The other marker names (synonyms) are stored in the database and can be visualized in the Marker Details window.

Physical Maps

Physical maps are based on nucleotide sequences. Above a certain level of zoom the annotated genes are displayed as separate horizontal bars representing sets of exons. At this scale a click on the gene or exon will bring up a Gene Details window.

A region of a physical map can also be explored in the Sequence view where multiple tracks are displayed horizontally along with the sequence. To select the region on the map, hold the Ctrl key and left mouse, drag the mouse across a region of interest. This will display an arrow corresponding to the orientation of the sequence (green arrow if the plus strand is selected, red arrow if the minus strand is selected). Click the arrow to show a window with the sequence. If the size of the selected region exceeds 1,000,000 bp, an additional message box is shown asking to confirm the lengthy operation.

Note

It is possible to select regions larger than 1 million bp; however, fetching the sequence will take longer.

 

Select sequence