### Secondary Structure Prediction

1. Close all windows and open the alignment at https://www.jalview.org/tutorial/alignment.fa. Use the [ESC] key to ensure no sequences are selected.

2. Select Web Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JPred Secondary Structure Prediction from the alignment menu. A status window will appear and after some time a new window that includes the JPred prediction will appear. The results from the prediction are visible in the annotation panel below the alignment. JPred secondary structure prediction annotations are examples of sequence-associated alignment annotation.

3. Return to the original alignment, select the sequence FER_MESCR by clicking on the sequence ID. Select Web Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JPred Secondary Structure Prediction from the alignment window menu.

4. Compare the number of sequences in both of the Jpred alignments with the original alignment.
Note: There are several hundreds of sequences in the second prediction, compared to 15 sequences in the other two alignments. The reason is that when a single sequence is selected, JPred performs a PSI-BLAST search to expand the prediction dataset before it runs the prediction.

5. Compare the jnetpred annotation when the Jpred predictions are calculated from a single sequence, FER_MESCR, with the jnetpred annotation when the whole alignment is used.

6. Annotations can be renamed by right-clicking the mouse when the cursor is placed on the annotation label panel and selecting Edit label. And exported by selecting Export Annotation from the same annotation context menu. The exported annotations can be drag-and-dropped onto different alignment window to aid comparison.

The annotation panel can get quite busy during this exercise.
(i) Annotations rows can be hidden by right-clicking the mouse in the annotation label panel and selecting the “Hide This Row” option in the context menu.
(ii) The Annotations drop-down menu in the alignment window provides options for reordering and hiding alignment-related, sequence-related and auto-calculated annotation.

For more information on this topic go to section 8.1 of the Jalview manual.
This exercise can be viewed in the Secondary structure prediction of proteins video.