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

If your sequence was called “MyPUC,” it will be divided into two sequences, called
“MyPUC 5’ end” and “MyPUC 3’ end.”
Duplicating a sequence
You can duplicate a sequence fragment. To do this, highlight the icon, then go to the
Edit menu and choose Duplicate Seq Fragment. Sequencher will use the name of the
original fragment as a basis for the new fragment’s name. If the fragment you want to
duplicate has a chromatogram associated with it, Sequencher will ask whether you also
want to duplicate the chromatogram or duplicate the sequence without chromatograms.
Click on the appropriate button to proceed.
If you wish to cancel the operation, simply press the Cancel button. Chromatograms
occupy a lot of memory but Sequencher uses a very efficient algorithm to compress
trace data. However, we suggest that you only duplicate the text if you don’t need the
chromatograms. (See Chapter 15 “Chromatograms” for more information.)
Reverse and Complement
The data you bring into Sequencher may not necessarily be in a particular biologically
relevant orientation. To change the orientation of the sequence, go to View and choose
Reverse & Comp. Sequenced Strand. To display the original orientation, go to the
View menu and choose Sequenced Strand.
Note: You will always have two copies of your data in Sequencher, the original data and
the edited version. This duplication allows you to revert to the original data, as discussed
in more detail below.
About experimental data
Creating a baseline
Sequencher notes the original base sequence when you import your data so that after
editing the sequence, you can still discard all of your edits and revert to the baseline
(experimental) data. You can also do this for sequences that you enter from the keyboard.
When you close a Sequence Editor that has not had its data recorded as experimental
data, the program explicitly asks whether the contents of the Sequence Editor should
be recorded as experimental data (see Figure 8-4). Click on Record As Experimental
Data if you are finished editing the sequence. If you are not finished, click the Not Yet
Finished button.
Figure 8-4 The Record as Experimental Data dialog box
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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