Selecting sequences for scanning

The scanning is started from the Toolbox:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | RNA Structure (Image rna_folder)| Evaluate Structure Hypothesis (Image graph)

This opens the dialog shown in figure 22.25.

Image structure_scanning_step1
Figure 22.25: Selecting RNA or DNA sequences for structure scanning.

If you have selected sequences before choosing the Toolbox action, they are 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 adjust scanning parameters (see figure 22.26).

Image structure_scanning_step2
Figure 22.26: Adjusting parameters for structure scanning.

The first group of parameters pertain to the methods of sequence resampling. There are four ways of resampling, all described in detail in [Clote et al., 2005]:

The second group of parameters pertain to the scanning settings and include:

The third parameter group contains the output options: