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

Note: When a sequence becomes part of a contig the data are automatically recorded as
experimental data if they have not previously been stored in that form.
Once a version of the sequence has been recorded as experimental data, all future changes
are considered to be “edits” to it. As a data quality tool, all such edits can be marked in
color and displayed in Bold Magenta or lower-case text. This feature is invoked in the
View menu under the Base Edits As command. The default is set to Bold Magenta but
you can also choose Not Highlighted or bOLD & cASE cHANGE.
Resetting a baseline
If you decide that some of the original data was incorrect (perhaps a simple typing error
that has been corrected in the “edited” version of the sequence), go to the “Experimental
Data” version of the sequence by clicking the Show Experimental button and then click
the New Baseline button.
Note: Setting a new baseline for a sequence resets all of the bases to a not-yet-edited
state. None of the bases that were edited will appear in Bold Magenta letters.
Viewing experimental data
After you enter a new sequence, Sequencher archives a copy that is “locked” (not
editable). In the course of assembling your data, you may make a great number of edits
to any particular sequence. This locked version enables you always to refer back to
the sequence as it was originally entered. To see the Experimental Data version of the
sequence click the Show Experimental button in the Sequence Editor button bar.
Reverting to experimental data
If you edit a sequence incorrectly, you can delete all the changes to that sequence and go
back to the archived baseline. To do so, open the Sequence Editor . Then choose Revert
To Experimental Data from the Sequence menu.
If you edit a contig incorrectly, you can delete all the changes to an individual sequence
and go back to the archived baseline. To do so, open the contig editor. Select the sequence
by clicking on its icon which can be found on the left hand side of the contig editor.
You can now remove the sequence from the contig by using the Remove Selected
Sequences… from the Contig menu. Then choose Revert To Experimental Data from
the Sequence menu. You can then reselect the fragments and rebuild the contig.
Viewing experimental data for Chromatograms
If your data came from an automated sequencer, click the button labeled Show
Chromatogram to view the experimental data of a sequence. This will display the
original trace data. Sequencher allows you to scroll either vertically (the default) or
horizontally. To change the scroll orientation, click the appropriate button in the left
bottom corner of the fragment chromatogram window. (See Chapter 15 “Chromatograms”
for more information.)
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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