Alignment Window

Conservation Bars & Sequence Logos

Left-clicking on the small view above the alignment enables/disables the conservation visualization. By default it is disabled for performance reasons. A right click toggles between the visualization modes, which are conservation bars and sequence logos.

Sequence List

By right clicking on the sequence list left to the alignment, a context menu pops up. Items within this context menu allow you deleting, importing and exporting sequences from/to the alignment. Reordering of the sequences can be done using the Rearrange Sequences palette.

Toolbar

Modi (Video-Tutorial)
	selection mode. In this mode you can highlight different regions in the alignment. Use the remove selection button to clear the selection.
	edit alignment mode. In this mode you can insert and remove gaps. You can choose out of three different cursors, which are described in the Cursors to edit alignments section. If the sequence part of the alignment is focused, you can also add/remove symbols to correct the sequences. Please note that 4SALE keeps secondary structures valid at all time, so if you delete a symbol taking part in a binding, 4SALE automatically removes the corresponding binding information from the secondary structure.
	edit structure mode. In this mode you can manually edit the secondary structure information of each sequence. Hovering the secondary structure symbols, the cursor is changing to visualize the current available function. The green plus sign indicates that a bond can be inserted at this point, a minus shows up when the bond (including the corresponding bond position) will be removed on mouse click. To insert a bond click on the first binding position and then its corresponding position, 4SALE will assist finding the corresponding binding position, by changing the cursor. Note that this mode preserves valid secondary structures (this mode is only available when secondary structure data is present).
Cursors to edit alignments (Video-Tutorial)
	standard cursor. This cursor behaves like the cursor known from text editors.
	left side cursor. All insertions and deletions will occur at the beginning of the sequence. This cursor can be used to shift the complete sequence to the left or right.
	exclusive cursor. Modifications using this cursor will affect all sequences excluding the selected ones.
Selection
	complement selection. Toggle this button to enable/disable complement selection in select mode. Complement selection is active by default. Please note that this affects all selections including search results and selections made in the structure viewer. If it selects more than you expect, please disable it.
	ignore gaps. Activate this checkbox to ignore gaps in select mode. Gaps within the selection-area, will not be highlighted, when this box is checked.
Automatically align
	align. You can choose your preferred alignment method, from the pull down menu. Please note that 4SALE has no influence on remote services and they probably would not run properly.
Clear selection
	clear selection. Use this button to clear all selected regions.
Add secondary structure information
	manually add structures. Use this button to open the sequences in a sequence & secondary structure window to manually add their according secondary structure information (see edit structure mode). The initial alignment will contain no binding information. This Video-Tutorial shows how to use this feature.
	remote structure prediction. Use this button to predict the secondary structures with remote tools.
Zooming
	zoom out. Use this button to get a better overview of large alignments.
	zoom in. Use this button to enlarge the alignment.