CLC Genomics Workbench enables the user to simulate the separation of nucleotide sequences on a gel. This feature is useful when designing an experiment which will allow the differentiation of a successful and an unsuccessful cloning experiment on the basis of a restriction map.
There are several ways to simulate gel separation of nucleotide sequences:
- When performing the Restriction Site Analysis from the Toolbox, you can choose to create a restriction map which can be shown as a gel (see Restriction Site Analysis).
- From all the graphical views of sequences, you can right-click the name of the sequence and choose Digest and Create Restriction Map (). The sequence
will be digested with the enzymes that are selected in the Side Panel. The views
where this option is available are listed below:
- Circular view (see Circular view view).
- Ordinary sequence view (see View sequence).
- Graphical view of sequence lists (see Sequence lists).
- Cloning editor (see Cloning editor).
- Primer designer (see Primer designer).
- Separate sequences on gel: To separate sequences without
restriction enzyme digestion, first create a sequence list of the
sequences in question, then click the Gel
button () at the bottom of the view of the sequence list (figure 21.47).