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 below picture we can see a few minor changes to the contig editor.
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. 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.
![[picture]](contig_editor.join.gif.html)
(Click for full size image)
This page is maintained by
James Bonfield.
Last generated on 29 April 1996.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_61.html