For the color display, you can specify the color for each nucleic acid base or amino acid residue. You can assign amino acid residues to color groups according to their chemical properties. Alternatively, residues can be colored according to degree of consensus among the sequences at each position. In addition, you can create and apply your own color schemes.
To choose or edit a color group, select the color group button in the MSA editor window. The Color Group Editor dialog box is displayed. The Color Group Editor dialog box is basically the same for protein and nucleotide sequence alignments, but some of the Color By drop-down menu options are different.
These groupings are based on the degree of consensus among the aligned sequences at each position.
The Consensus Identity option uses three colors:
- 100% Identity - where all the sequence residues match the consensus, then the 100% Identity color is used for the entire column
- Consensus Match - where one or more residues in a column do not match the consensus, those that do match will be displayed in this color
- Mismatch - this color is used for all the residues that do not match the consensus.
The % Consensus option colors residues according to the percentage of residues at a given position that share the same symbol. The color displayed depends on the residues in the other sequences, not on the calculated consensus.
When there is a protein alignment in the MSA editor window, you can select a range of preset color groups that are based on chemical or physical properties of the residues. The Color By drop-down menu includes the following property options:
- Alpha-helix
- Alpha-helix + P450
- Hydrophobicity + Charge
- Acidity + Basicity
- Structural Position
- Steric Bulk
- Chou-Fasman Alpha Helix
- Chou-Fasman Beta Sheet
- Levitt Alpha Helix Forming
- Levitt Beta Sheet Forming
- Levitt Turn Forming
- Dayhoff Matrix
- Functionality
- Gascuel & Golmard
- Helix Termintors
- Chamical Type
The default option for protein alignments is Chemical Type. When you choose a color group from the menu, the corresponding groups are displayed in the Color Group Editor dialog box.
The default property groups used by ClustalW alignment are included as a Color By option for protein alignments. These groups are unusual in that a given amino acid can appear in more than one group, and therefore could be represented by more than one color. To simplify the MSA Editor tab, these groups are always shown in white.
TO SPECIFY individual residue colors
1. With nucleotide or protein sequences displayed in the MSA Editor window, click the color group editor button.
The Color Group Editor dialog is displayed.
2. If you are using DNA sequences, ColorBy is setto DNA Residues by default. If you are using protein sequences, set Color By to Smooth Scaling.
3. To alter the color scheme, choose a color for each residue from the drop-down color palette to the right of each residue symbol.
Alternatively, use the system Color Picker to select a color, by clicking on the current color swatch.
4. Select Apply to preview the changes. If they are not satisfactory, select Revert to restore the previous color set.
5. Select OK to save the changes.
TO APPLY an existing residue color scheme
1. With nucleotide or protein sequences displayed in the MSA Editor window, click the color group editor button.
The Color Group Editor dialog box is displayed.
2. Choose a preset color scheme from the Color By drop-down menu.
3. Select Apply to preview the changes. If they are not satisfactory, select Revert to restore the previous color set.
4. Select OK to save the change to the display.
1. With nucleotide or protein sequences displayed in the MSA Editor window, click the color group editor button.
The Color Group Editor dialog box is displayed. You can now choose a preset color scheme to use as a template for your own scheme,as follows:
2. Choose a scheme from the Color By drop-down menu.
3. Choose Copy This Group from the Color By drop-down menu.
A New Color Group Name prompt is displayed. The default name will be Copy of Name, where Name is the scheme you selected.
NOTE: You can modify a preset scheme, but we recommend that you always make a copy of the scheme to modify, because you can delete it later if necessary.
4. Type a name for the new scheme, and select OK to return to the Color Group Editor dialog box.
5. Edit the residue groups as required. For each group you create, do the following:
- type a name for the group
- type the IUPAC one-letter code for each residue in the group
- choose a color for the group from the drop-down palette.
NOTE: Each residue type can only appear in one group. If you enter a residue that already appears in another group, it is automatically removed from the previous group.
6. Select Apply to preview the changes. If they are not satisfactory, select Revert to restore the previous color set.
7. Select OK to save the changes.
1. With nucleotide or protein sequences displayed in the MSA Editor window, click the color group editor button.
The Color Group Editor dialog box is displayed.
2. Choose the user-defined color group that you want to rename or delete from the Color By drop-down menu.
NOTE: You cannot use the Color Group Editor to rename or delete the pre-defined color groups.
3. Do one of the following:
- To rename the color group, choose Rename This Group from the Color By drop-down menu. A prompt to enter a New Color Group Name is displayed. Type the new name in the text box, and select OK to return to the Color Group Editor
- To delete the color group, choose Delete This Group from the Color By drop-down menu.
4. Select OK to close the Color Group Editor dialog box.