Creating Features

1. Close all windows and open the file https://www.jalview.org/tutorial/alignment.fa.

2. The cysteine residues at columns 97, 102, 105 and 135 are known to be involved in iron binding. To annotate them as features, navigate to column 97 and select the entire column by clicking on the ruler bar above the sequences. Right-click on a residue within the selection to open the context menu and select Selection $\Rightarrow$ Create Sequence Feature. A dialog box will appear, enter a suitable feature name such as “Iron binding site” and group name such as “Iron binding Cysteine” and press OK. The features will then appear on the sequences.

3. Roll the mouse cursor over the new features in the alignment. Note that the information given in the tool tip is the feature name and residue number, not the column number.

4. To demonstrate that the feature is linked to the residue, clear all selections by pressing [ESC]. Hold down the [SHIFT] key, then place cursor on a residue to the left of the new feature, insert a gap at column 95 by moving the mouse to that position by clicking and dragging the mouse to the right. The feature has moved with the sequence. Roll the mouse cursor over the feature in the sequence and note the feature number. Delete the gaps you created using Edit $\Rightarrow$ Undo. Place the mouse cursor over the residue with the feature again and note the feature number.

5. Add a similar feature to column 102, 105 and 135. When the Features dialog box appears, clicking the Sequence Feature Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.

6. Select View $\Rightarrow$ Feature Settings. . . from the alignment window menu. The Sequence Feature Settings dialog box opens, move this so that you can see the newly created features. Untick the check box for “Iron binding site” in the Show column and note that this feature is no longer visible on the alignment. Click the check box again to display the feature.

7. Click the coloured box under ‘Colour’ and use the Select Colour dialog box to change the colour of the feature.

8. Close the Sequence Feature Settings dialog box by clicking OK.

9. Select View $\Rightarrow$ Show Sequence Features from the alignment window menu to toggle all sequence features off and on.