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

Figure 12-4 Fill Void dialog box
Deleting bases from the 5’ or 3’ ends
Although you may have automatically trimmed your sequences for poor quality data
when you imported them (see Chapter 6 “Preparing your data for assembly”), you may
still need to delete a few 5’ bases to correct any mistakes made during the amplification
process.
Select the bases you want to delete. If you are at the 5’ (left end) then click the Forward
Delete key. Sequencher will delete those bases without moving the entire sequence to
the left. Similarly, if you choose bases on the 3‘ (right) end use the Backspace key and
Sequencher will automatically delete those bases without realigning your sequence.
Note: When editing from the consensus line you do not have to worry about the bases
shifting to the left and right.
Inserting gaps or bases into a contig
If you want to insert gaps, go to the Sequence menu and click on Insert Gaps &
Move Bases then choose Right or Left from the submenu. You can also create gaps by
selecting a number of bases equivalent to the gap size you want to create. Press the Tab
key if you want the selected bases to move to the right. To move to the left, hold down the
Alt key when you press Tab. The space created will be filled with gap marks (small colon
marks) that will appear without disrupting the rest of your contig.
Once your gaps are in place you can either type the bases you want into the gap using
Overstrike When Editing mode or use the lasso and grabber tools to move existing bases
into the new position.
Making edits from the consensus line
You can simultaneously edit all the bases in the column above the position you choose in
the consensus line, instead of individually changing each one. To do this, select a base in
the consensus line and enter the character that represents the edit you want to make in that
column. If you currently have a base selected in a sequence fragment, go to the Select
menu and choose Contig Column (Ctrl+K).
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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