Introduction to the cloning editorIn the cloning editor, most of the basic options for viewing, selecting and zooming the sequences are the same as for the standard sequence view. See View sequences for an explanation of these options. This means that e.g. known SNP's, exons and other 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. At the right-hand side, you can select whether or not to select a vector. When no vector has been selected a button Change to Current is enabled. This button can be used 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. This is explained in details below.
- At the bottom, there is a panel where the selection of fragments and target vector is performed (see elaboration below).
There are essentially three ways of performing cloning in the CLC Genomics Workbench. The first is the most straight-forward approach, which is based on a simple model of selecting restriction sites for cutting out one or more fragments and defining how to open the vector to insert the fragments. This is described as The cloning workflow. The second approach is unguided and more flexible and allows you to manually cut, copy, insert and replace parts of the sequences. This approach is described under Manual cloning. Finally, the CLC Genomics Workbench also supports Gateway cloning.