In the cloning editor, most of the basic options for viewing, selecting and zooming the sequences are the same as for the standard sequence view (View sequences). In particular, this means that annotations can be displayed on the sequences to guide the choice of regions to clone.
However, the cloning editor has a special layout with three distinct areas (in addition to the Side Panel found in other sequence views as well):
- At the top, there is a panel to switch between the sequences selected as input for the cloning. You can also specify whether the sequence should be visualized as circular or as a fragment. On the right-hand side, you can select a vector: the button is by default set to Change to Current. Click on it to select the currently shown sequence as vector.
- In the middle, the selected sequence is shown. This is the central area for defining how the cloning should be performed.
- At the bottom, there is a panel where the selection of fragments and target vector is performed.
The cloning editor can be activated in different ways. One way is to click on the Cloning Editor icon () in the view area when a sequence list has been opened in the sequence list editor. Another way is to create a new cloning experiment (the actual data object will still be a sequence list) using the Cloning () action from the toolbox. Using this action the user collects a set of existing sequences and creates a new sequence list.
The cloning editor can be used in two different ways:
- The cloning mode, when the user has selected one of the sequences as 'Vector'. In the cloning mode, the user opens up the vector by applying one or more cuts to the vector, thereby creating an opening for insertion of other sequence fragments. From the remaining sequences in the cloning experiment/sequence list, either complete sequences or fragments created by cutting can be inserted into the vector. In the cloning adapter dialog, the user can switch the order of the inserted fragments and rotate them prior to adjusting the overhangs to match the cloning conditions.
- The stitch mode, when the user has not selected a sequence as 'Vector'. In stitch mode, the user can select a number of fragments (either full sequences or cuttings) from the cloning experiment. These fragments can then be stitched together into one single new and longer sequence. In the stitching adapter dialog, the user can switch order and rotate the fragments prior to adjusting the overhangs to match the stitch conditions.