The Genetic Map IV
Highlight
The Highlight button at the top of the genetic map window has a submenu (rightmost button) that can be used to highlight - or even make invisible - a subset of markers on the genetic map. The subset can be defined in several ways. For example, by using the Template box in the ACeDB main window you could restrict the genes shown in the genetic map window to those starting with the character "t". But a much more powerful application of this utility allows the results of a query to be highlighted. The accompanying figure shows how this can be done.
The development of a query starts at the AAtDB main window. One of the pull-down menu items available in that window is called Query. Choosing it will cause the Query window to appear; this window is visible in the upper right of the figure.
Clicking on the New KeySet button in the Query window causes a second window (called Query Answer) to appear. This is where the results of the query will eventually be placed. When the window first appears it will be empty.
The query we demonstrate here is designed to locate all members of the Gene class that satisfy two criteria: they must have a DNA sequence associated with them, and they must also have a genetic map position defined. The query language follows certain precise rules and you can click on the Help button in the Query window to find out more information. For now click (with the leftmost mouse button) on the line below the "Direct Query Commands" prompt and type in the query exactly as shown. Press the return key when you are finished typing. In a few moments the Query Answer window will display the members of the Gene class that satisfy the search criteria.
We now move to the final step. In the genetic map window, click Highlight with the rightmost mouse button and drag down to "Highlight selected keyset". Markers in the Query Answer window which are on this genetic map display are now highlighted in violet. If you click on Highlight and instead, drag down to "Keep only Highlighted objects", all the markers on the genetic map which were not located by the query will be hidden. Finally, clicking on Highlight and dragging to "Clear and show all" causes the map to revert to the default view, in which everything is visible.
Drag
The Drag button is used to construct what are called private maps. In effect, this feature makes it possible to copy the genetic map and then change the map position and confidence of any marker . The result can be saved for future reference - i.e., as a private map. We will not discuss private maps in more detail, but you may want to experiment with them. Consult Help for more information.