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

In either case, the method you choose to calculate your consensus can affect your results.
Generally, using the command Consensus Inclusively will report more variants than
Consensus by Plurality.
Sequencher recalculates the consensus on the fly, so if you change the methods you are
using to compute your consensus, you can reconstruct the Variance Table quickly. Just
click on the Refresh button in the button bar at the top of the Variance Table to display
the results of the new consensus calculation.
For more information on consensus calculations, see Chapter 11 “The Contig Editor”.
Variance Table Options
If you need to change User Preferences for your Variance Table click the Options button
in the Variance Table button bar. The User Preferences dialog opens in a new window.
(See Chapter 21 “Customizing Sequencher and User Preferences” for more detailed
information.
Working with the Variance Table
Navigating a Variance Table
To navigate through any form of Variance Table, use the arrow keys to move across the
rows or down the columns.
When you are working with any Variance Table and only want to focus on differences,
use an arrow key with the Alt key. This will skip any cells that match the comparison
sequence. If you try to move the cursor beyond the edge of the table, you will be alerted
by a beep.
Note: If you are using the Compare Consensus to Reference command, you will
see the consensus base(s) for each contig you have selected in the same position. If you
are using the Compare Translation to Reference command you will be viewing the
consensus codon for each contig you have selected in the same position.
Sorting the Variance Table
The Variance Table’s Sort functions are useful when, for instance, you need to segregate
clone sequences that perfectly match your Reference Sequence or cluster sequences of
like alleles (see Figure 13-14). The Variance Table simultaneously displays differences
and calculates summary information about your selections. The Table lists the total
number of differences for each sequence at the bottom of that sequence’s column. The
Variance Table also displays the total number of differences for each position to the right
of each row. There are two Total buttons, at the bottom left and top right corners of the
Variance Table. These act as Sort buttons.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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