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If the corresponding document is not locked, it is possible to edit the a sequence:
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The Edit sequence submenu is available in the Actions main menu and in the Sequence View context menu. Also you can use the corresponding shortcuts.
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Editing mode and annotations settings
To switch on the editing mode for the sequence, select the Edit sequence button on the left toolbar of the Details View:
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Description of the dialog parameters:
Paste data here — you must input the inserted subsequence. This parameter is mandatory.
Annotated regions resolving mode — defines either to Expand affected annotation, Remove affected annotation, Split (join annotation parts) or Split (separate annotation parts) in case when the subsequence is inserted to the sequence position where some annotations are presented.
Recalculate values of qualifiers - recalculates regions in qualifiers when sequence is modified.
Position to insert — the sequence position where to insert the subsequence.
Save to new file — the result sequence can be saves to a new file instead of modifying the current file. You must select the Document location. FASTA and Genbank file formats are available when you do not include annotations to the result file. If you check the Merge annotations to this file item, the annotations will also be saved to the result file (Genbank file format is only available in this case).
In case a subsequence has been selected, the Replace subsequence is available from the context menu or by the Ctrl+R shortcut. The dialog opened in this case is similar to the dialog described above, except it already contains the sequence to be edited an doesn’t allow to input the start position.
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A special cursor appears in this case, and the sequence can be edited as in a text editor:
- To insert characters to the sequence, move the cursor to the required location and type the characters or paste them using Ctrl + V / Cmd + V keyboard shortcut.
- To replace a sequence region, select it and insert the new characters.
- To remove a character from the sequence, move the cursor to the required location and press Backspace or Delete. To remove a region, select it and press one of these shortcuts.
One can also configure the way how annotations located in an edited region should be modified. To open a dialog with the settings select Edit–>Annotations settings on sequence editing in the Actions main menu or in the context menu of the Sequence View.
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Select one of the
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following:
Region to remove — specifies the region of the sequence that will be removed in the form. This parameter is mandatory.
Annotated regions resolving mode— specifies what to do with annotations that overlap with the region that is removed. You can select either Crop corresponding annotation (i.e. make it smaller) or Remove corresponding annotation.
Recalculate values of qualifiers - recalculates regions in qualifiers when sequence is modified.
Save to new file — similar to the same parameter in the Insert subsequence dialog (described above).
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- Expand or crop affected annotation — an annotation located in an edited region is expanded in case of characters insertion or cropped in case of characters deletion.
- Remove affected annotation — all annotations in an edited region are removed.
- Split (join annotation parts) — an annotation is split into two join elements (see "The DDBJ/ENA/GenBank Feature Table Definition" for details).
- Split (separate annotation parts) — an annotation is split into two annotations.
It is also possible to check the Recalculate values of qualifiers option in the dialog. If it is selected, qualifiers of all annotations are parsed on the sequence editing. Qualifiers values that specify coordinates (like "100..200") are re-calculated accordingly to the sequence modification. For example, the value might become "104..204", if four characters have been inserted before the corresponding annotation.
Getting reverse-complement, reverse, or complement sequence
To replace a sequence with its reverse-complement sequence, select Edit–>Reverse-complement sequence in the Actions main menu or in the context menu of the Sequence View. The keyboard shortcut for this action is Ctrl + Shift + R / Cmd + Shift + R.
Use the Reverse sequence or Complement sequence items in the same menus to replace the sequence with its reverse or complement sequence.