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