The Physical Map I
When the physical map appears, it is centered on the chs clone, which is selected (highlighted in red). In general the map will be centered upon whatever clone was selected to access the map in the first place. Notice that two other items on the map have been highlighted in a fainter color (a text remark, and directly above it, a small rectangle). These objects have been highlighted in this way because they are related to the chs clone.
Although the identity of the clones vary from contig to contig, the overall layout of the physical map display will be the same. That is, certain regions of the physical map display are reserved for certain kinds of information. We will now describe some of these regions in the accompanying figure, starting from the top of the window.
The physical map's title bar shows that this contig has been placed on chromosome V. For some contigs, coordinates are given in the title bar which are an estimate of the contig position on the chromosome genetic map. The title bar does not always give this kind of information and may at times omit the chromosome or coordinates, depending on how much is known about the contig.
Below the title bar is a series of horizontal lines, each one identified by a label (in parentheses) at the center of the line. These represent YAC clones and this space is reserved for them. The shorter lines below the YACs represent cosmids. Notice that the cosmid labels are handled differently from the YAC labels; this difference (plus their reserved location in the window) identifies these as cosmids rather than YACS. Below the cosmids a single small rectangle indicates that one of the clones in the contig has a sequence associated with it. It is currently highlighted in pink because of its association with the chs clone (it would otherwise be yellow). Sequences associated with the contig will always appear in the area below the cosmids, but above the thick horizontal green line. Moving down a bit, the text in pink highlight indicates a remark with an association with the chs clone.
Some of the cosmids are marked with an asterisk and some are represented by thicker lines than others. A cosmid with an asterisk is canonical - i.e., it is known to be similar or identical to other (buried) cosmids which are not drawn on the map. Cosmids drawn with thicker lines have been gridded onto hybridization filters that are being used to complete the Arabidopsis physical map.
Most of the objects in the physical map window can be doubled-clicked to bring up additional information in new windows. Clicking on YACs and cosmids will bring up text windows, while clicking on a sequence rectangle will create a sequence window. In addition, if you click only once on a clone, YAC, sequence, or genetic map symbol, any item on the physical map that is "connected" to the item clicked will be highlighted in a pale pink.
The physical map, like any ACeDB window, has its own pop-up menu. We have pulled it down to emphasize the Quit and Help options once again.
Next we discuss methods for recentering a physical map or for changing the magnification of the view.