Multiple alignment picture display

The Multiple Alignment Picture window displays the multiple alignments in PDF format. The quality of this view is to publication standard and can be easily copied and pasted into other applications, for example word processors or graphical editing applications.

When you create an alignment from annotated protein sequences, then the Picture tab will display a colored box around any common domains.

TO MODIFY the Multiple Alignment Picture window

1. In the MSA Editor window, select the Prefs button
2. Select the Picture Fonts tab.
3. Select the font style, size, and weight for the text with the Set button.
4. Enter a title for the window in the Title text box.
5. Choose a numbering style for the alignments, using one of the Numbering radio buttons.
6. Type in the required number of residues per line in the Line Length text box.
7. Select Apply to see the effects of your changes on any open MSA editor windows.
8. Select the Picture Shading tab.
   • If you want similar residues to be treated as identities for the purpose of shading, select the Treat similarities as identities check box.
   • Choose the appearance of residue highlighting for identities, using the controls in the Identities panel.
   • Choose the appearance of residue highlighting for similarities and mismatches, using the controls in the Similarities and Mismatches panels.
   • Note that identities and similarities are calculated using the currently selected colour group in the main editor tab.
9. Select Apply to save the changes and close the dialog box.
10. Alternatively, select Defaults to restore the default values, or Cancel to close the dialog box without saving.

TO MODIFY the consensus line in the Picture window

To view the options for calculating and displaying the consensus line, select the Consensus tab in the Multiple Alignment Options dialog box. The consensus line controls are the same for both Picture Display and MSA editor display windows.

Related Topics.

Displaying multiple alignments

MSA Editor

Multiple alignment text display

Pairwise alignment text display

Displaying shared domains across protein alignments.