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

Select command
Table 15-1 Summary of Select commands
Contig
Next Ambiguous Base
Next Contig Disagree
Next Edited Base
Next Low Confidence
Base
Next Met To Stop (>0bp)
Ambiguous bases, Disagreements, First base in large
gap run.
Disagreements
Edited bases
Any consensus base that is derived from a low
confidence base
Any pair of Start and Stop codons in one of forward
ORFs.
As you move your selection from each position that requires scrutiny to the next, you
are likely to need to repeat these commands frequently. Therefore, Sequencher creates
a shortcut for that command in the space bar after the first time you invoke a Next
command. Press the space bar to move from one selected base to the next candidate.
To change any Next command to search in the reverse direction, combine the command
with the Shift key.
Editing bases from traces
Now that you can easily locate the bases that need attention, you can edit your data in
either the contig editor window or the chromatogram display. As you edit, both windows
update automatically. (Refer to Chapter 12 “Editing Contigs” for more information on
editing.)
To edit a base while viewing a chromatogram, click on the current base call (upper line
of text) you want to edit, then type the new base call (Figure 15-6). You can also select
multiple bases for deletion by dragging the cursor across them.
Figure 15-6 Clicking on a base displayed in a trace
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved. 142