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

15. Chromatograms
In this chapter you will learn how to use the chromatograms from an automated
sequencer to help you when editing your contigs. We discuss how Sequencher displays
traces and secondary peaks to find heterozygotes and how you can edit bases from traces
or revert to experimental data.
Working with automated sequencer data
When you import a trace file from an automated sequencer, Sequencher imports the
chromatograms and the confidence values if these are available.
Note: If you import a text file containing just ASCII characters, you will not have
imported traces. To import traces you must import the trace file. Text files from an
automated sequencer will be only a couple of kilobytes in size, whereas trace files will be
well over 50 kilobytes.
When you copy a Sequencher project file from one machine to another, you don’t need to
copy the trace files separately because Sequencher stores the trace information along with
everything else in the project file. Sequencher compresses the imported traces to conserve
disk space, so don’t be alarmed if a project file containing several sequences from an
automated sequencer is smaller than any one of the trace files.
Viewing chromatograms from a Sequence Editor
Sequencher’s chromatogram display is tightly integrated with its other editors. You can
view the entire original trace for a sequence fragment by opening the Sequence Editor
for that sequence. Click the Show Chromatogram button in the button bar or go to the
Window menu and choose Chromatogram. You can scroll either vertically (the default)
or horizontally. To change orientation, click the appropriate button in the left bottom
corner of the fragment chromatogram window.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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