The Stop Codon Map plots the positions of all the stop codons on one or both strands of a contig consensus sequence. It can be invoked from the gap4 View menu. If the Contig Editor is being used on the same contig, the Refresh button will be enabled and if used will fetch the current consensus from the editor, repeat the search and replot the stop codons.
The figure shows a typical zoomed in view of the Stop Codon Map display. The
positions for the stop codons in each reading frame (here all six frames are
shown) are displayed in horizontal strips. Along the top are buttons for zooming, the crosshair toggle, a refresh
button and two boxes for showing the crosshair position. The left box shows
the current position and the right-hand box the separation of the last two
stops codons selected by the user. Below the display of stop codons is a
ruler and a horizontal scrollbar. The information line is showing the data for
the last stop codon the user has touched with the cursor. Also shown on the
left is a copy of the View menu which is user to select the reading
frames to display.
Positioning the cursor over a plotted point will cause its codon and
position to appear in the information line.
It is possible to find the distance between any two stop codons.
Pressing the left mouse button on a plotted point will display "Select
another codon" at the bottom of the window. Then, pressing the left
button on another plotted point will display the distance, in bases,
between the two sites. This is shown in the box located at the top right
corner of the window.
If the Contig Editor (see section Editing in gap4) is
currently running on the same contig as is being displayed as a Stop
Codon Map, the Refresh button will be shown in bold lettering and hence
be active, otherwise it will be greyed out. Pressing the button will
fetch the current consensus from the Contig Editor and replot its stop
codons. Hence the plot can be kept current with the changes being made
in the editor.
![[picture]](stops.unix.gif.html)
(Click for full size image)
Examining the Plot
Updating the Plot
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staden-package.
Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_40.html