4SALE - A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing

Philipp N. Seibel, Jörg Schultz, Tobias Müller, Thomas Dandekar & Matthias Wolf

Department of Bioinformatics, Biocenter, University of Würzburg, Germany

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Toolbar
Structure Inspector
4SALE Palettes

### Toolbar

Modi
| selection mode. In this mode you can mark 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. there are also different cursors available.
| edit structure mode. In this mode you can manually edit the secondary structure information of each sequence. Note that this mode preserves valid secondary structures (this mode is only with secondary structure data available).
Cursors to edit alignments
| standard cursor.
| left side cursor.
| exclusive cursor.
Select complement
| complement selection. Toggle this button to enable/disable complement selection in select mode. (this button is only with secondary structure data available)
Automatically align
| align. Here you can choose your preferred alignment method. Please note that 4SALE has no influence on remote services. They probably would not run properly.
Clear selection
| clear selection. Use this button to deselect 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).
| 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.