Reverse complements of sequences

CLC Genomics Workbench is able to create the reverse complement of a nucleotide sequence. By doing that, a new sequence is created which also has all the annotations reversed since they now occupy the opposite strand of their previous location.

To quickly obtain the reverse complement of a sequence or part of a sequence, you may select a region on the negative strand and open it in a new view:

        right-click a selection on the negative strand | Open selection in New View (Image open_selection_in_new_view)

By doing that, the sequence will be reversed. This is only possible when the double stranded view option is enabled. It is possible to copy the selection and paste it in a word processing program or an e-mail. To obtain a reverse complement of an entire sequence:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Nucleotide Analysis (Image nucleotideanalyses)| Reverse Complement (Image reversecomplement)

This opens the dialog displayed in figure 15.3:

Image reversecomplementdialog
Figure 15.3: Creating a reverse complement sequence.

If a sequence was selected before choosing the Toolbox action, the sequence is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements.

Click Next if you wish to adjust how to handle the results. If not, click Finish.

This will open a new view in the View Area displaying the reverse complement of the selected sequence. The new sequence is not saved automatically. To save the sequence, drag it into the Navigation Area or press Ctrl + S (Image command_key_web + S on Mac) to activate a save dialog.