The overview and DNA view take up most of the main window (see the section called A breakdown of the main Artemis edit window). Both views act in a very similar way, so they are described in the same section. In particular they both show the forward and reverse strands of the sequence and a representation of the three translation frames in each direction. The forward sequence is read from the EMBL entry, the reverse sequence is derived from the forward one by complementing it. In the overview shows only the stop codons of each translation frame, but in the DNA view the shows the complete six frame translation.
The horizontal scrollbar controls which part of the sequence is currently visible. The scroll bar at the left controls the zoom level.
To select a feature just click on it with the first mouse button. This will unselect anything that is currently selected. To add a feature to the selection rather than replacing the current selection, hold the shift key while clicking. A single feature can be removed from the selection in the same way, because shift-clicking acts as a toggle. The situation is made slightly more complicated by the existence of spliced genes. When a feature segment (exon) is added to the selection the feature that contains the segment is implicitly added as well. When the last segment of a feature is removed from the selection, the feature is implicitly removed.
A single base or amino acid can be selected simply by clicking on it. A range of bases can be added by clicking on the base at one end of the range then shift-click on the base at the other end of the range. Alternatively you can drag out a range of bases: click on a base then hold the mouse button down and move to the other end. To select a complete open reading frame (ORF), double click the middle mouse button (see the section called Notes on Using The Mouse) anywhere inside the ORF (see the section called Open Reading Frame for another way to select an ORF).
See the section called The Selection in Chapter 1 for more about the selection.
Double clicking on a feature with the first mouse button causes both views and the feature list to centre themselves on that feature. Similarly, double clicking the first mouse button on a base or amino acid will centre both views on that base/amino acid.
A double click of the middle mouse button on a feature will open an edit window for that feature. This is the same as clicking once and then choosing the Edit Selected Features menu item (see the section called Edit Selected Features).
The pop-up menu is activated by pressing the third mouse button (see the section called Notes on Using The Mouse) on a feature view. The menu is split into three sections. The top contains functions that will act on the current view. The middle contains shortcuts to some of the main window menus. The bottom contains four toggle buttons which influence the appearance of the view.
Note that not all of these functions are available all the time (the first two are only shown when there are some selected features).
Raise Selected Features. Raise the selected features so that they appear in front of all other features.
Lower Selected Features. Make the selected features go behind all the other features.
Smallest Features In Front. Sort the visible features so that the smallest features appear in front of the larger ones. This is only necessary when the user has manually rearranged the features using "Raise Selected Features" or "Lower Selected Features".
Zoom to Selection. Scroll and scale the display so that the current selection is centred and full width.
Select Visible Range. Select the currently visible bases on the forward strand.
Select Visible Features. Select those (and only those) features that currently visible in this view. Any features that are off screen or have been filtered out with the "Set Score Cutoffs ..." control.
Set Score Cutoffs ... The score cutoffs panel allows the user to filter the features of the active entries so that features with low or high scores are not shown. The "score" of a feature is the value of the /score qualifier and should be a number from 0 to 100. The cutoffs window has two sliders. Any feature that has a score less than the value of the top controller or more than the value of the bottom controller will not be shown. Features with no /score qualifier will always be shown.
This toggle button controls whether the feature labels are displayed on their own line (when the toggle is on) or on the top of the features (when the toggle is off). The default setting for this toggle can be set in the options file (see the section called feature_labels in Chapter 4).
This toggle controls whether the entries are shown in the context of the three frame translation or one entry per line on screen. In the first case the entries will be overlaid, in second case they will be shown in parallel. The default setting for this toggle can be set in the options file (see the section called one_line_per_entry in Chapter 4).
This toggle button controls whether or not to show the 3 frame translation of the forward sequence.
This toggle button controls whether or not to show the 3 frame translation of the reverse sequence.
Toggle the display of start codons in the view. See the section called Eukaroytic Mode in Chapter 2 to find out how to change which start codons to use.
Toggle the display of stop codons in the view.
Toggle the display of directional arrows on each feature. The default setting for this toggle can be set in the options file (see the section called draw_feature_arrows in Chapter 4).
Toggle the display of black borders around each feature. The default setting for this toggle can be set in the options file (see the section called draw_feature_borders in Chapter 4).
Normally non-protein features are drawn on the DNA lines. This toggle allows the user to force all features to be drawn on the frame lines, which can sometimes improve readability. The default setting for this toggle can be set in the options file (see the section called features_on_frame_lines in Chapter 4).
If selected the sequence and features will be drawn on screen as if they are reverse complemented with the first base to the right of the screen.
This toggle turn base colouring on or off. (Note that this feature is completely unless, it exists for amusement only).
Moving the horizontal scrollbar will change the part of the sequence that is visible. The position of the view can also be changed by using the Goto menu (see the section called The Goto Menu), by double clicking the first mouse button on a feature in one of the sequence views or in the feature list or by double clicking on a base or amino acid.
The vertical scrollbar at the right edge of the view controls the scale - moving the scrollbar up will zoom in and moving the scrollbar down will zoom out. When the scrollbar is at the top (at it's most "zoomed-in" position), the complete six frame translation is shown. Otherwise only the stop codons are shown. The main difference between the overview and the DNA view is that the DNA view initially shows the full translation, whereas the overview shows only the stop codons. The other difference is that the labels are on in the overview by default (see the section called The Pop-up Menu).
The direct editing option (See the section called Enable Direct Editing in Chapter 2) enables the user to change the start or end position of a segment by dragging it around with the mouse. This works best in the DNA view window. As an example, to move the start position, click the mouse button on the first base of the feature or exon, hold the button down, move the mouse pointer to the desired position, then release the button.