View Options in Sequence View
“Which options for viewing and displaying are available in sequence view?”
The following options can be changed to alter the display of your DNA files in sequence view. Sequence view can be selected from the bottom navigation bar and the view/display settings can be found in the top banner under the “View” tab. Note that when a view setting is toggled on the respective button is shaded blue and when it is off the button is grey. If a view option is not available in the sequence view it is completely grayed out (both the background and the icon appear in gray).
- Features:
To toggle on/off the feature display, use the “Features” button. By default this is toggled on.
- Feature Names
To toggle on/off the overhead display of feature names above features whose name does not fit within the feature label, use the “Features Names” button. For small features this will display the name of the feature between the feature and the sequence.
- Open Reading Frames (ORFs)
To toggle on/off open reading frame display, use the “ORFs” button. By default this is toggled off for all maps. Open reading frames are displayed as arrows on the map indicating directionality. Additionally in sequence view you will notice the amino acid translation is displayed for ORFs and the ORF arrow will have dots at Methionine (start) positions.
- Enzymes
To toggle on/off enzyme display, use the “Enzymes” button. By default enzymes are toggled on and are displayed in black text above the sequence. When a restriction enzyme is selected, the restriction site is highlighted and the cut site will be displayed in blue. You can select which types of enzymes are shown by using the dropdown on the “Enzymes” button to select between unique cutters, dual cutters, type IIS enzymes, non-cutters or a custom enzyme list you have created.
- Primers
To toggle on/off primer display, use the “Primers” button. By default all primers are displayed. Primers appear in orange above or below the sequence depending on if they are forward or reverse primers, additionally directionality is shown by the primer arrow.
- Display
To toggle on/off horizontal sequence display use the “Display” button. This will display the whole sequence horizontally.
- Translations
To toggle on/off amino acid translations use the “Translations” button.
NEEED TO UPDATE THIS WITH NEW AMINO ACID TRANSLATION FEATURES THAT PHILLIPE BUILT IN !!!!!!!!!!!!!!!!!!!
- DNA Colors
To toggle on/off DNA colors use the “DNA colors” button. This will color code the entire sequence with Adenine (A) = Green, Thymine (T) = Red, Cytosine (C) = Blue and Guanine = Yellow.
- Rotate to Cursor
To change the origin or starting point of your file, first select the new desired starting point by clicking it on the map (notice a grey indicator line will show the position and the location will be displayed in the bottom left). Then use the “Rotate to Cursor” button to make this the new origin point. Note that this effectively changes the origin and is not solely a view function.
- Reverse Complement
To change the complementarity of your DNA sequence (to flip it) use the “Reverse Complement” button. Note that this changes the orientation and will be saved to the file.
- Information
To view the DNA file’s associated information, use the “Information” button. This will open a panel on the right-hand side where you can edit and view all data.
- Split View
To use multiple navigation views simultaneously you can use the “Split View” button. Alternatively, you can use the split screen icon to the right of the bottom navigation bar. This will split the screen and allow you to select any of the navigation views from the bottom navigation bar. Note any changes or selections made on one side of the screen will also be made on the other.
