Tutorial: Auto Annotation

Building on the foundation of AutoFeature file (Tutorial 21) introduced in GCK 4.0, AutoAnnotation is a new extension that when turned on, provides a link between a GCK construct file and an AutoFeature file. Choosing the menu option Construct > Features > AutoAnnotation… brings up the same dialog allowing a user to choose an AutoFeature file, and have those defined features marked in a construct. Now however, the Construct and the AutoFeature file will be linked.

  1. Start GCK 4.5
  2. Open the file ‘Bluescript_KS-PLUS.gcc’ from the Tutorial Files folder by choosing File > Open…
  3. Select Construct > Features > Auto Annotation… menu option to bring up an Open dialog.
  4. Navigate to the Tutorial Files folder to select the file titled Common Features.gcf and press Open.
  5. GCK will use the features defined in the Common Features file to searchBluescript_KS-PLUS for matches, and will apply the associated formatting. The result should be as in Figure 7.3.

Figure 7.3: Bluescript_KS-PLUS Annotated

A check mark will be placed beside the Auto Annotation… selection under the Construct menu (for both Mac and Windows), indicating the feature is turned on, and the Construct and AutoFeature file are in-sync (Figure 7.4).

Auto Annotation Menu

Figure 7.4:  Auto Annotation Menu

* Additionally, in the Mac version of GCK, the AutoAnnotation toolbar icon will show as a green circle, with a check mark (Figure 7.5).

Figure 7.5: Toolbar – Auto Annotation ‘On’


6. Now let’s make a change to the underlying sequence. Double click on the green arrow, pointing counter-clockwise around 11:30, to select the range. This region represents the Ampicillin resistance promoter. Choose Edit > Cut to remove.

7. A dialog indicating the selected operation will delete one or more comments pops up. Press OK to proceed. The segment is removed, and a junction marker is placed where the two ends were re-joined.

8. If GCK discovers a change to either the DNA sequence of the Construct or any modifications to the linked AutoFeature File, the menu flag will change from a check mark (✓) to a diamond (♦) in the Mac version, or a dot (•) under Windows, to indicate that the files may no longer be in sync.

Figure 7.6: Menu – AutoAnnotation Out of Sync

In the Macintosh version of GCK, the Auto Annotation toolbar icon will also change to a yellow triangle, with an exclamation mark.

Figure 7.7:  Toolbar – AutoAnnotation Out of Sync

9. Pressing the toolbar button (Mac) or selecting the menu item Construct > Features > Auto Annotation… will produce a dialog (Figure 7.8):

Figure 7.8:  AutoAnnotation Confirmation Dialog

10. Pressing ‘No’ returns to the GCK construct. Pressing the Yes button will re-scan the construct and mark the features stored in the linked AutoFeature file accordingly. The AutoAnnotation menu flag (and toolbar icon in the Mac version) will be restored to a check mark (✓) to indicate that the Construct and AutoFeature file are again in-sync.

In our example, there are no ‘new’ features that were identified, or existing features that were removed, but the Auto Annotation menu is now refreshed (Figure 7.9)

Figure 7.9: Auto Annotation Rescanned


Users may choose to work with multiple AutoFeature files, for identifying various elements in a construct. By linking AutoFeature files with GCK constructs, users can be sure any underlying DNA sequence changes in the GCK file – or additions / modifications / deletions in the AutoFeature file itself – can be identified early, to avoid costly mistakes in the lab.

You can learn more about AutoFeatures in the “AutoFeature Window” chapter, beginning on page 7-1 of the current GCK manual.

This concludes the tutorial. Close any open windows, but do not save any changes you may have made so that others may work with these sample files.

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