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

Figure 16-8 Checkmarked enzyme list
If you are interested in enzymes with special characteristics, such as blunt ends or 3’
overhangs, explore the commands in the Select menu within the dialog.
Start by choosing Select None to clear all selections. Each menu item you choose
after that will add all of the enzymes with the specified characteristic. Selections are
cumulative—no command (except Select None) removes any enzymes from the list.
If, for example, you want all the enzymes that recognize sequences either 4 or 5 bases in
length, choose Select None followed by 4-base and then 5-base.
When you are finished selecting enzymes, click OK in the lower right corner of the dialog
box or press the Return key. Sequencher redraws your restriction map with the newly
selected enzymes.
Changing the default enzymes
To change the default enzyme selections for items in a project, select the fragments or
contigs you want to change. Go to the Window menu and choose Specify Restriction
Enzymes while viewing the Project Window. Sequencher will warn you if no sequences
are chosen. The enzymes you choose at this time are now the default set for any selected
sequences or contigs in your project.
Adding and editing enzymes
Sequencher lets you add new enzymes to the list. Go to the top of the enzyme editor and
select Allow Changes. All the sliders will now change from gray to blue. Click on New
Enzyme to open a blank entry in the enzyme editor. Note that the OK button changes to
Done.
You can now enter information in the Enzyme Name and Recognition Sequence fields.
When you click Done, Sequencher adds the new enzyme to the list in alphabetical order.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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