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The Join Editor

When joining two contigs we use the join editor. This is simply a pair of contig editor displays stacked above one another with a "differences" line in between. Looking at the picture below we can see a few minor changes to the contig editor.

[picture]
(Click for full size image)

Firstly, we have a Lock button. When set (as it is in the illustration) scrolling either contig by using the scrollbar or the four movement buttons will also scroll the other contig in unison.

The Align button aligns the overlapping consensus sequences and adds pads appropriately. This can be seen in the illustration at location 2654, where a pair of pads have been added to the bottom editor. Note that it is essential to align both the contigs over the full length of the overlap. It is much more difficult to achieve this after the join has been made. It should be noted that each editor display maintains it's own undo history and hence using align may well add to both undo histories. In this case, to undo the align command the undo button must be used in both editors.

When quit is pressed a dialogue box is displayed containing information on the total overlap percentage mismatch. You are then asked whether you wish to perform the join. For joins above a certain mismatch (20 percent by default) a second confirmation is required.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_62.html