Annotating Alignments

Annotating Alignments

  1. Close all windows and open the file

  2. Right-click on the label name of the Conservation annotation row to bring up the context menu and select Add New Row. A dialog box will appear asking for Annotation Name and Annotation Description. Enter “Iron binding site” and click OK. A new, empty, row appears.

  3. Navigate to column 97 with the cysteine amino acids. Select column on the new annotation row called “Iron binding site”, and right click, select Label from the context menu, enter “Fe” in the box and click OK. Right-click on the selection again, select Colour, and choose a colour from the Choose Colour dialog box then click OK. Press [ESC] to remove the selection in the alignment.

Note: depending on your annotation sort settings, your newly created annotation row might “jump” to the top or bottom of the annotation panel.

  1. On the annotation row, select columns 70-77. Right-click and select Sheet from the context menu and press OK. A new line showing the sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet arrow. Select column 20-30, right-click and select Helix from the context menu and press OK.

  2. In the annotation label panel, place the mouse on the name of the newly created annotation row. Right-click the mouse and select Export Annotation in the context menu. In the Export Annotation dialog box that opens, select the Jalview format and click the [To File] button, save the file on the computer.

  3. Open the file in a text editor. Edit the text by changing the name of the annotation row and save the file.

Note: The format for this file is given in the Jalview help. Press [F1] to open it ([F1]-[Fn] (Mac)), and find the “Annotations File Format” entry in the “Alignment Annotations” section of the contents pane.

  1. Drag the edited file onto the alignment and look for the new entry in the annotation panel.

  2. In the alignment window menu, select File $\Rightarrow$ Export Annotations… in the Export Annotation dialog box that opens, select the Jalview format and click the [To Textbox] button. Compare to the single annotation row file saved previously.

For more information on this topic go to section 4.1 of the Jalview manual.
 This exercise can be viewed in the Annotation rows video.