Note that a current limitation means that only single read based contigs can be edited. All file based contigs cannot be edited. This means all reference contigs.
Note that all editing uses overwrite mode rather than insertion mode. However, if you hold down the OPTION key, then gaps or residues can be inserted instead.
- The numbering over the consensus sequence is in ungapped coordinates. Gaps are not included in the numbering, or in the locations shown in the Features Table.
- You can edit any of the sample sequences (in either the upper or lower pane). As you type, the consensus sequence is updated in real time. If you delete the last non-gap character at a position, the gap will close up.
- You can copy any selection of more than one residue.
- To remove a sequence from the alignment, click on the title button to select the entire sequence and press the <delete> key.
- Most actions are "undoable" to a single level. Note that if you are editing very large assemblies, certain actions (e.g. deleting one or more sequences) may be sluggish while a copy is made of the assembly to allow a later undo.
- Deletions at either end of a sequence are considered "true" deletions and the residues will be actually deleted, rather than replaced by gaps.
The following keys may be used to edit the alignment.
- any IUPAC letter replaces the base.
- any IUPAC + OPTION inserts that base
- Space bar or '-' replaces the base with a gap.
- OPTION + space bar or OPTION + '-' inserts a gap.
- double-click on a read to select the entire sequence, then the cursor keys will "nudge" the read left or right. This only works for a selection of the entire sequence, and will not nudge exons or introns.
- [delete] or [backspace] replaces the base with a gap.
The contig editor window is highly interactive. All of the sequence residues can be edited, although there are some restrictions that simplify the use of the editor:
- To delete a residue, overwrite it with either a <space> or a "-" character. The consensus will be updated dynamically. If all overlapping sequences have a gap at that location, the gap will be closed up.
- Although you can copy any number of residues, pasting is disabled for all sequences.
- You cannot perform a block selection of the sample sequences - only one sample sequence can have residues selected at any one time (although you can select multiple sample sequences to remove them from the assembly).
- You can only overwrite residues in the consensus sequence. You cannot insert residues.