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 direct editing option 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. (See the section called The Options Menu in Chapter 2).
To select a feature from the list 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 The Selection in Chapter 2 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 popup menu is activated by pressing the third mouse button (see the section called Notes on Using The Mouse) on a feature view. The menu contains shortcuts to some of the main window menus and a four toggle buttons.
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 in the overview by default (see the section called The Pop-up Menu).