Shuffle sequence

In some cases, it is beneficial to shuffle a sequence. This is an option in the Toolbox menu under General Sequence Analyses. It is normally used for statistical analyses, e.g. when comparing an alignment score with the distribution of scores of shuffled sequences.

Shuffling a sequence removes all annotations that relate to the residues. To launch the tool, go to:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | General Sequence Analysis (Image generalsequenceanalyses)| Shuffle Sequence (Image shuffle)

This opens the dialog displayed in figure 13.5:

Image shufflesequencedialog
Figure 13.5: Choosing sequence for shuffling.

If a sequence was selected before choosing the Toolbox action, this 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 to determine how the shuffling should be performed.

In this step, shown in figure 13.6:

Image shufflesequencedialog2
Figure 13.6: Parameters for shuffling.

For nucleotides, the following parameters can be set:

For proteins, the following parameters can be set:

For further details of these algorithms, see [Clote et al., 2005]. In addition to the shuffle method, you can specify the number of randomized sequences to output.

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 shuffled 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.