Structural information can also be used to provide the sequence alignment with its color scheme. For example, the alignment shown in Figure 2.6A is shown in the color scheme "ClustalW". Beneath the alignment is the display of the transmembrane prediction for the alignment. In Figure 2.6B, the alignment is shown in the color scheme designated by the transmembrane prediction data.

The four structural information color schemes available are as follows:

1. Transmembrane topology
2. Secondary structure
3. Ranked data (blue/green)
4. Ranked data (red/yellow)

To apply these structural information color scheme, choose the Set color scheme from structure... option from the Display options menu. This will open a structural information-type selection window. After you have selected the data type, you need to select the file that has structural information for each sequence in FASTA format. This is the same file you can use for the structural alignment display. The color scheme for the selected data type will be applied to the alignment as interpreted from the structural data. This color scheme may be changed by either choosing another MSA or structural color scheme or by clicking on the Remove color button.