You can customize the appearance of the text view, both as it appears on the screen and as it will be printed. The formatting enables you to control:
- the number of residues that occur per sequence block, between sequence numbers, and between sequence marks
- how the sequence itself is displayed: uppercase or lowercase letters, single- or double-stranded format
- which feature types will be included among the annotations to the sequence
- which translated feature types will have their amino acid sequences printed beneath the nucleic acid sequence.
Annotated sequence formatting also affects some of the format properties of the aligned sequence display.
This functionality may be accessed at any time, whether an annotated sequence window is present or not. If an annotated sequence window is present, it will be updated immediately to reflect changes.
The layout of the sequence can affect the clarity of the displayed information, depending on how much feature information is also visible.
1. Choose MACVECTOR | PREFERENCES and choose the TEXT VIEW tab.
2. Type a number in the Line Length text box to specify the number of residues per line.
3. Type a number in the Blocking text box to draw residues in groups of that number.
4. Type a number in the Numbering text box to number the sequence residues at that interval.
5. Type a number in the Marking text box to place an asterisk (*) at that interval along the sequence.
This is often done at half the interval of the Numbering value.
6. Select the Letter case as upper or lower as required.
7. Select the display of amino acid codes as one or three letters when a nucleic acid sequence translation is displayed.
8. Select either single or double to display a nucleic acid sequence as either a single- or double-stranded molecule.
10. Select OK to apply the formatting.
When the sequence is displayed, you can control the type of features that are shown beneath the sequence. The features must be present in the features table of the sequence.
1. Choose MACVECTOR | PREFERENCES and choose the TEXT VIEW tab.
2. In the Show panel, select check boxes as required.
Selected features that occur in the sequence's features table will appear as annotations to the sequence in the display.
3. Select OK to apply the formatting.
The features are displayed below the appropriate residues in the sequence.
NOTE: If one or more features overlap, they appear below each other.
You can also view the translation of certain features, if they occur in the sequence's features table. These features are:
- mature protein product (mat_peptide)
- protein coding region (CDS)
- signal peptide (sig_peptide)
- exon regions (exon).
1. Choose MACVECTOR | PREFERENCES and choose the TEXT VIEW tab.
2. In the Translate panel, select check boxes as required.
3. To display the translated region in codon groups, select block to phase.
This display style overrides the Blocking value set for the remainder of the sequence.
4. Select OK to apply the formatting.
Translatable features of the selected types are displayed in translated form beneath the main sequence.