This module predicts structures with maximum and near maximum expected accuracy. These are structures that maximize pair probabilities.
The scoring function used is:
score = gamma*(sum of pair probabilities for pairs) + (sum of unpairing probabilities for unpaired nucleotides)
Predicting Maximum Expected Accuracy Structures
- First choose a save file from a previous partition function calculation. Click the button labeled "Partition Function Save File." A dialog box will open to get the name of a PFS file.
- A default name is provided for the output file that will contain the predicted structures. This can be changed by clicking the "CT File" button.
- Change the weight given to pairs by editing the default value for "Gamma." The default is generally the best option.
- Change suboptimal structure parameters by changing the appropriate values under "Suboptimal Structure Parameters." The maximum number of suboptimal structures is controlled by both the "Max % Score Difference" and the "Max Number of Structures." Structures are generated until either the max number of structures is reached or the scores differ by greater than Max % Score Difference from the optimal score. "Window" controls how different the structures are from each other. A higher Window will generate structures that are more different and a small Window (such as zero) will result in structures that are more subtly different.
- Press the "Start" button.
- When the calculation is complete, you will be asked whether to draw the predicted structure on the screen.