Selecting sequences for
evaluation
Start the Evaluate Structure Hypothesis tool by going to:
Tools | Classical Sequence Analysis (
) | RNA Structure (
)|
Evaluate Structure Hypothesis (
)
This opens the dialog shown in figure 26.22.
Figure 26.22: Selecting RNA or DNA sequences for evaluating structure hypothesis.
If you had selected sequences before running the tool, those sequences will be listed in the Selected Elements pane of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements. Note that the selected sequences must contain a structure hypothesis in the form of manually added constraint annotations.
Click Next to adjust evaluation parameters (see figure 26.23).
Figure 26.23: Adjusting parameters for hypothesis evaluation.
The partition function algorithm includes a number of advanced options:
- Avoid isolated base pairs. The algorithm filters out isolated base pairs (i.e. stems of length 1).
- Apply different energy rules for Grossly Asymmetric Interior Loops (GAIL). Compute the minimum free energy applying different rules for Grossly Asymmetry Interior Loops (GAIL).
A Grossly Asymmetry Interior Loop (GAIL) is an interior loop that is
or 
where 
(see
http://mfold.rna.albany.edu/doc/mfold-manual/node5.php)
- Include coaxial stacking energy rules. Include free energy increments of coaxial stacking for adjacent helices [Mathews et al., 2004].