Help on Editing Bases And Alignments with the Alignments Editor
There are single and global editing functions within the alignments editor, accessed either by placing the cursor on a single base on a single sequence line and then
using the editing buttons (Trim, Insert, Delete, Shift, Suck)
or by selecting areas of sequence with the mouse and dragging the selection, or a combination of the two (ie select area - use editing button).
The global editing functions are generally mediated by editing the 'consensus' or 'reference/guide' sequencing line at the top of the alignments
or by drag selecting sequence across multiple sequence lines using the mouse
The editing buttons fire repeatedly while they are pressed.
Additional editing functions such as 'Anti-Parallel' - which flips the entire alignment to the reverse complement (consensus mode only), 'Insert Sequence', or
'Re-align' are available via the 'Alignment Options' or 'Edit' menus.
Some editing functions can be assigned keyboard shortcuts (hotkeys) using the menu option 'File' -> 'Assign keyboard shortcuts'
Editing Bases
Place the cursor on the single base (or gap) to be edited and type a replacement base (or gap) on the keyboard.
If you edit the top 'consensus' or 'guide' sequence line in the alignment, all corresponding positions in the other sequence lines are edited as well.
You can fine tune the position of a base call in the trace by selecting the base,
then holding down the Alt key on the keyboard and using the left and right arrow keys to move the base on the trace
Deleting bases by 'trimmimg' sequence ends
The 'TRIM' editing buttons are useful for removing poor sequence quality sections on the 5' or 3' end of a sequence run
'Trim >' deletes all the bases to the right of the cursor while
'< Trim' deletes all the bases to the left of the cursor
To globally trim all sequences in the alignment, place the cursor in position on the top 'consensus' or 'guide' sequence line and use the trim buttons
Deleting or Inserting Bases or Gaps
You can insert or delete gaps/bases using the 'Insert' and 'Delete' editing buttons.
A '<' or '>' indicates on which side of the text editing cursor the insert or delete will occur.
'Insert >' inserts a gap on the right of the cursor
'< Insert' inserts a gap on the left of the cursor
'Delete >' deletes the base/gap on the right of the cursor while
'< Delete' deletes the base/gap on the left of the cursor
You can also insert gaps at the start and/or end of the alignments by placing the cursor on the required end and using the appropriate 'Insert' button.
You can then type additional bases on the top line to globally add sequence to the start/end of all sequences in the alignment.
An alternative is to use the 'Edit' -> 'Insert Sequence' menu options
Moving bases across or out of extended gaps
'Suck >' sucks a base from across a gap that is on the right of the cursor while
'< Suck' sucks a base from across a gap that is on the left of the cursor
Suck is useful if your sequences have large gaps in them (such as spliced sequences) as the alignment tends to spread bases inappropriately across the gaps.
You may also shift the whole sequencing line left or right by selecting '< Shift' or 'Shift >' respectively.
More on select/drag editing'
if you use the lower display 'translate all', in 'Ignore Gaps' mode - you can no longer select across multiple sequence lines.
If you use 'respect gaps' mode, you can both select across multiple lines and drag within the protein alignment.
The 'Jump' button jumps you 5' - 3' to the next sequence mismatch.
Changes can be reversed by pressing the Undo button.
Press the 'Save' button to save changes you have made to the bases and alignments. Note that the data is saved in the DNADynamo file and does not edit the data in the original sequencing files.
Press the 'Standard Window' button to return to the main DNADynamo sequence window, which either contains the 'Guide/Reference' sequence, or displays the 'Consensus' sequence, depending upon the mode.