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

Editing the information for a sequence or contig
You can annotate the sequence by clicking anywhere in the Comments: box and typing
the information. To store more information than the Comments: box allows, go to the
Edit menu and choose Edit Comments…. Sequencher opens a small text editing window
that stores about 250 characters of text for each sequence. After you have added text with
Edits Comments… a small “I” (for “Info”) appears in the upper left corner of the icon.
If you want to remove the information in the Comments: box, select the text and then go
to the Edit menu and choose Contents from the Clear option.
The Project Window button bar
The button bar contains buttons for frequently-used commands. It appears just below
the top of the Project Window. You can use the smaller left-hand button, which has an
up arrow on it, to hide the button bar. Click on the button and the button bar will “hide”
behind the title bar.
When the button bar is hidden, you can still see the bottom of the left-hand button under
the title bar. It will show a down-pointing arrowhead. Click on the arrowhead and the
button bar will reappear.
If you click on the Assembly Parameters button this will display the Assembly
Parameters window. Clicking on the AbN button will enable the Assemble by Name
function. Assemble Automatically, Assemble Interactively and Assemble to
Reference are used to assemble sequences you have selected. If AbN is enabled then
the Assemble Automatically and Assemble to Reference buttons will have different
labels. If you select a sequence and then click on the Trash Can button, that sequence
will be removed from the project.
Templates
A template is a special type of project that can be set with your choice of parameters
and preferences. Templates can contain ordinary sequences or a Reference Sequence.
Preferences can include Feature settings, enzyme sets, and display settings. With
templates, you can also set Assembly Parameters, Assemble by Name handles and
Trim parameters. These will be discussed later in this manual.
A template can be used as a new project or imported into an existing project. You can
use templates to set up standard operating procedures and methods to reuse or distribute
throughout your lab.
Save Project As Template
You can save any project as a template by using the Save Project As Template
command. Set the User Preferences and parameters that you want to use. You can
include a Reference Sequence or ordinary sequences.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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