Predicting with Pred2ary

Select a jury from the Jury menu, then click on "Predict" to predict the secondary structure.

Predictions may take about a second per jury, so you should see a progress window telling you what's going on.

Once everything is done, the main window should display the predicted secondary structure, and also a graph of the predictions, if the "graph predictions" checkbox is checked.

Below the sequence or sequences, you will see a list of letters representing the predicted secondary structure at each position. 'H' means alpha helix, 'E' means extended beta strand, and '-' means everything else. The predictions are color coded, with H's in red, E's in green, and -'s in blue. The shade of the color should be lighter for more likely predictions, and darker for less likely ones.

If the "graph predictions" checkbox is checked, a graph of the probabilities of helix, strand, and coil will be shown below the predictions. The three lines on the graph are color coded as above. The vertical scale ranges from 0% to 100% chance of each type of secondary structure. If you want to know the exact numbers at each position, these can be seen by saving in the default (YAPF) format.

The structural class of each protein is also predicted. This is shown in the Log Window.