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Plotting Stop Codons

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.

(Click for full size image)

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.

Examining the Plot

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.

Updating the Plot

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.

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This page is maintained by staden-package. Last generated on 22 October 2002.