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

How to import using menu commands
Importing sequences
Sequencher imports sequences in a variety of text and chromatogram formats. Some of
the most popular are ABI, MegaBase, CEQ, SCF, GenBank, EMBL, DDBJ and plain text
files.
To import a sequence, first bring the Project Window to the front by clicking on it. Under
File menu, choose Import. Choose Sequences… and then browse to and select the file
you want to import. Click the Open button in the lower right area of the dialog box or
press the Return key. You may need to select a file format from the drop down menu
called Files of Type: in order to see the files of interest in the dialog window. To see all
the files in a particular location choose All Files (*.*).
You can also select from a Folder of Sequences…, ACE Project…, CAF Project…,
GCG contig…, Sequencher project… or Sequence from VecBase…. (Working with
specific formats is discussed below.)
If Sequencher cannot import the file you will get a warning message to that effect.
Importing GenBank features
When you import a sequence in GenBank format, you will automatically import the
features, including the location, the feature keys and feature qualifiers. The feature key
used in sequences published in GenBank, EMBL and DDBJ describes the biological
nature of the annotated feature or indicates information about changes to the sequence.
(For more information on features and feature keys see Chapter 17 “Motifs and Features”
and Appendix 27 “Feature keys and qualifiers”.)
Where feature locations described in the GenBank file are ambiguous, Sequencher will
warn you that it cannot import these features and will list the features in a dialog box you
can print out for your records.
Importing lists of sequences
Sequencher’s functionality has been modified to take advantage of the Windows file
system. If you use the Import menu item with the suboption Sequences… you can select
multiple files for a single import command. To select a continuous list of sequences,
choose the first sequence in the list and then, holding down the Shift key, select the last
sequence in the list. The import window selects the two sequences and all of the files in
between. Click the Open button to import all of the selected sequences in to your project.
To select a discontinuous list of sequences, hold down the Control key while clicking on
the file. Click the Open button to import all of the selected sequences into your project.
The Files of Type: drop down menu allows you to filter the files that are displayed in the
file browser. The filters are With Chromatogram Sequences, Without Chromatogram
Sequences, Supported File Formats and All Files (*.*). You may see some files
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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