Outlining Shared Domains in Aligned Sequences

Multiple Sequence Alignments retain feature information from their individual input sequences and can use this information to outline shared domains in the aligned sequences.

To identify/display common domains in an alignment

1. Individually annotate the sequences you want to align.
2. Ensure the domains/features you are interested in are visible.
3. Set the Fill color to the color you would like to see in the alignment.
4. Add the sequences to a multiple sequence alignment document and align or, keep the single sequence documents open and choose Analyze | Align Multiple Sequences Using....
5. Click on the Mode toolbar button in the Editor tab and select Show Features

A bar will appear above every sequence in the MSA Editor tab where you can see the extent and color of the features. When you switch to the Picture tab, you will see colored outlines around the shared domains.

The Features tab in the protein multiple sequence alignment window allows you to view, edit, create and/or delete features in each of the aligned sequences.

When the Editor or Picture tabs are active, a floating Group Palette is displayed (similar in concept to the Graphics Palette for the single sequence Map tab), allowing you to turn features on and off permitting greater control over how shared domains are displayed and outlined.

Related Topics.

Displaying multiple alignments

Picture tab

Domain coloring

MSA Editor

Multiple alignment text display

Pairwise alignment text display