Objective

To box, shade and annotate an alignment.

Background

To become familiar with the ICM Alignment Editor.

Instructions

1. First let us place a red box around the conserved cysteine residues. To do this click and drag over the residues in the alignment. Selected residues will be highlighted in blue. Right click on the selected residues and select .Draw Box. and select a color.
2. Now try to shade a region of your alignment. Select the residues as before. Right click on the selection and select Custom Color.
3. Now try annotating the alignment. Select the residues in the alignment in the same way as before. Right click on the selection and select Edit Comment / Line 1. Type the text in the box provided under the alignment. Note the length of text is limited by the length of the selection you made.

Notes and things to try:

• Try saving the alignment as an image. To do this, remove any blue selection and then right click and a menu is displayed. Select save as image there are three alignment style formats to choose.
• Try searching in the alignment for a particular sequence string using the right click menu.

Manual References (Web Links)

Alignment Editor