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 opened in the following ways:
- Click on the Cloning Editor icon () in the view area when a sequence list has been opened in the sequence list editor.
- Create a new cloning experiment using the Restriction Based Cloning () action from the toolbox. This tool collects a set of existing sequences and creates a new sequence list.
The Cloning Editor can be used in two ways:
- Cloning mode Opened when one of the sequences has been selected as 'Vector'. In this mode, you can apply 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 order and direction of the inserted fragments can be adjusted prior to adjusting the overhangs to match the cloning conditions.
- Stitch mode If no sequence has ben selected as 'Vector', a number of fragments (either full sequences or cuttings) can be selected from the cloning experiment. These can then be stitched together into a single new sequence. In the stitching adapter dialog, the order and direction of the fragments can be adjusted prior to adjusting the overhangs to match the stitch conditions.