Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

A locked editor is read-only. You cannot directly edit data, you can only view it.
However, if the sequence fragment has been incorporated into a contig, you can use the
contig editor to make changes. (See Chapter 12 “Editing Contigs”.)
Basic sequence editing
The Sequence Editor, shown in Figure 8-2, is a text processor that is specially optimized
to work with DNA sequences.
Figure 8-2 The Sequence Editor
The default system for coding in Sequencher is the IUPAC-IUB coding system. You can
define your own coding system for bases and ambiguities. (See Chapter 21, “Customizing
Sequencher and User Preferences” for details. The IUPAC-IUB codes also are included in
the appendix to this manual.)
The Sequence Editor works like any other text editor. The insertion point can be moved
using either the mouse or the arrow keys.
Note: If you hold down the Alt key and use an arrow key, the insertion point moves
three bases. If you hold down both the Ctrl and Alt keys, the insertion point moves nine
bases. If you hold down the Ctrl key and the up arrow, the insertion point moves to the
beginning of the sequence; if you hold down Ctrl key and the down arrow, the insertion
point moves to the end of the sequence.
The editor also performs typical operations including Cut, Copy, Paste and Undo. Use
the mouse to highlight a selection; hold down the Shift key and click elsewhere in the
sequence with the mouse to extend the selection.
There are also two commands for extending a current selection to the beginning or end of
a sequence, To Left End and To Right End, both located under the Select menu in the
Extend Selection submenu.
Once you have made a selection you can copy it by going to the Edit menu and using the
Copy Selection command. You can also cut the selection by using the Cut Selection
command, also located in the Edit menu.
The Paste function will remove non-sequence characters. You can define a sequence
character by going to the Window menu and then using the Ambiguity Editor in the
Ambiguity/Key Codes… option.
For instructions on trimming ambiguous data and vectors at the time you load your
fragments, see the chapters “Importing Data”, “Preparing Your Data for Assembly,” and
“Customizing Sequencher and User Preferences” elsewhere in this manual.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
50