Contigs are joined interactively using the Join Editor. This is simply a pair of contig editor displays stacked above one another with a "differences" line in between. Note that it is essential to align the contigs over the full length of their overlap. It is much more difficult to achieve this after a join has been made, and until the alignment is correct, the consensus sequence will be nonsense.
The few differences between the Join Editor and the Contig Editor can be seen in the figure below. Otherwise all the commands and operations are the same as those for the Contig Editor
One difference is the 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.
The Align button aligns the overlapping consensus sequences and adds
pads The alignment routine assumes that the two contigs are already in
approximately the right relative position (as they are immediately
after the Join Editor has been invoked from Find Internal Joins, or
Find Repeats). If they are not they must be positioned manually before
using the Align button.
The "<" and ">" buttons either side of the "Align" button
perform the alignment from the editing cursor to the start of the
contig and and from the cursor to the end of the contig
only. Alignment end-gaps are penalised at the curosr position but not
for the alignment end at the contig start/end position. These buttons
are useful for when multiple alignment positions may be valid, such as
is the case with an overlap consisting entirely of a STR.
It should be noted
that each of the pair of editors comprising the Contig Editor
maintains its own undo history, and using Align
is likely to add to both undo histories.
Hence, to undo the results of the Align command
the Undo button in both editors must be used.
Note also that storing the undo information takes up a great deal of computer
memory and slows down the alignment process. For this reason the settings menu
contains an option to turn off (or on) the saving of undo information. When
aligning very long overlaps it is advisable to turn off the undo saving.
When "Join/Quit" is pressed a dialogue box is displayed containing
the percentage mismatch of the overlap, and asking if the join should be made.
For joins above a certain
level of mismatch (20 percent by default) a second confirmation is required.
(Click for full size image)
Last generated on 25 November 2011.