You can customize the appearance of the alignment portion of the aligned sequence display, both as it appears on the screen and as it will be printed. This formatting does not apply to multiple sequence alignments, which have their own formatting options.
The aligned sequence formatting enables you to control:
- whether or not a query sequence line will appear
- the style and display of a score line
- how often the aligned sequences will be numbered and how often vertical alignment characters will appear
- the display of vertical and horizontal alignment characters
- the representation of matching and mismatching residues.
Characteristics of the query sequence are customized using the Format Annotated Display command (see the help topic "Formatting the annotated sequence display").
This functionality may be accessed at any time, whether an aligned sequence window is present or not. If an aligned sequence window is present, it will be immediately updated to reflect changes.
There are three possible components to an aligned sequence display:
- the aligned sequence
- the score line
- the query sequence.
If all three are present, they appear beneath each other in the order shown above.
The format of an aligned sequence affects the numbering of residues, representation of matched and mismatched residues, and visual alignment aids.
1. Choose Options | Aligned Display Options.
The Aligned Formats dialog box is displayed.
2. Type a number in the Numbering text box to number the sequence residues at that interval.
3. Type a number in the Vertical alignment text box to insert vertical alignment characters at that interval through the display.
This is an aid to keeping your place as you scan down through the aligned sequences. If you enter a zero in this box, no vertical alignment characters will appear.
4. Type a character in the vert. align. character text box to use as a vertical alignment character.
If you do not want any vertical alignment characters to appear, type a space in the box or leave it empty.
5. Type a character in the horiz. align. character text box to use as a horizontal alignment character.
This is an aid to keeping your place on the line as you scan left to see the sequence name. If you do not want any horizontal alignment characters to appear, type a space in the box or leave it empty.
NOTE: Do not use a hyphen, because MacVector uses hyphens to represent deletions and gaps in the aligned sequence.
6. From the Match Character panel, select the radio button corresponding to how you want to represent residues in the aligned sequences that match residues in the query sequence.
The character radio button enables you to enter a character of your choice in the text box.
7. From the Mismatch Character panel, select the radio button corresponding to how you want to represent residues in the aligned sequences that do not match residues in the query sequence.
The character radio button enables you to enter a character of your choice in the text box.
8. Select OK to apply the formatting.
Each aligned sequence display window is updated with the formatting changes.
Each character in the score line represents the score assigned to the comparison between the residue in the aligned sequence and the corresponding residue in the query sequence. This gives you a semi-graphical indication of which regions along the length of the sequence match the query sequence well and which match poorly.
1. Choose Options | Aligned Display Options.
The Aligned Formats dialog box is displayed.
2. Select the Score Line check box to display a score line beneath each of the sequences in the alignment.
3. Type a character of your choice in each of the boxes labeled +1 or greater, between -1 and +1, and -1 or less.
These characters can identify matching residues along the aligned sequence. Most scoring matrices give a positive score to an exact or equivalent match, and a negative score to a mismatch. Any or all of these boxes may contain a space character or be left blank.
4. Select OK to apply the score line.
Each aligned sequence display window is updated to include the score line.
The query sequence can be displayed beneath each of the sequences in the alignment. The format of the query sequence is controlled by the Format Annotated Display command (see the help topic "Formatting the annotated sequence display").
1. Choose Options | Aligned Display Options.
The Aligned Formats dialog box is displayed.
2. Select the Query Line check box to display a query line beneath each of the sequences in the alignment.
3. Select OK to apply the query line.
Each aligned sequence display window is updated to include the query line.