## Physical-map

This display represent the alignement of clones into contigs. (If you are using the C. elegans database, see help page on clone types).

Picking in the Yellow bar (when present) moves you to the sequence.

Picking in the lower Green bar moves you to the genetic map by local linear interpolation btween the nearest localised clones.

### Menu items:

- Quit: quits the window.
- Help: brings up this help.
- Print: prepares a Post Script file in ./PS (pmapxxx.PS) which you can then print on your local laser printer.
- Preserve: insure that the next pmap will be displayed in a different window, otherwise the present one will be reused.
- Redraw: useful from time to time if the window gets clogged accidentally after moving the window or following arrows.
- Recalculate: recomputes the display from the map data. Otherwise, the same display is shown again and again. We could make the recalculation automatic after any update of the clone tress but it would slow the program if you alter some data which do not actually influence the drawing.
- Show All Remarks: there are three categories of comments: General_, PCR_ and Y_. Typically, PCR_ and Y_ comments were used by John and Alan to help build the map (as are many General_ ones) and are not very useful to the rest of us. This switch is a toggle - turning on and off showing the extra comments.
- To Genetic Map: Moved to the real or estimated genetic position of the selected item.

Apart from the menu options, you can pick any clone and obtain it in text form, or pick the comments and the genes that may appear under the map. Using the arrow keys, you will move from one clone, comment or gene to the next.

The mid button recenter the display, slowly in the upper part of the window, faster in the lower part where a back bone of the physical map is shown.

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last edited: July 1994