Beckman Coulter CEQ 8000, User Manual

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CEQuence Investigator Procedures
212 CEQ™ 8000 Genetic Analysis System
Viewing Sequence Traces
When you first perform a comparison, you select one or two sequences to form the
consensus. Once the comparison is performed, the traces for these sequences are
displayed. When you click on any position in alignment view, the corresponding
peak(s) in the traces will move to the center of the trace view and will be framed by
two vertical lines.
When you first open or create a comparison, the traces will be scaled for ease of
readability. You may zoom each sequence pane individually and repeatedly by
clicking down on the left-hand mouse button, dragging the mouse pointer to form a
box around the desired area and then releasing the mouse button.
To unzoom both traces, click the
Unzoom All
button . The traces in both panes will
revert to a completely unzoomed state, displaying the entire range of the sequence
result(s).
To unzoom one of the two open data traces, right-click in the desired trace pane and
select
Unzoom Pane
. The selected trace will be unzoomed to display the entire range
of the result.
You cannot edit sequence traces in Sequence Investigator. However, sequence traces
can be edited in the Sequence Analysis module. If you use an edited result for your
comparison, your edited bases will appear in lower case.
Viewing Consensus Amino Acid Translations
When the system generates the comparison, it translates the consensus nucleotide
sequence into an amino acid sequence and displays it below the consensus sequence.
The amino acid translation starts at the first base relative to a reference codon. The
consensus is also segmented into codons, which are translated into their amino acids.
If edits occur in the consensus, a re-translation of the consensus amino acid translation
occurs automatically and the Discrepancy Map and the Differences line are updated
automatically.
Each codon will be shaded to show its boundaries. If a heterozygote occurs, the system
will note up to two possibilities; if more possibilities exist, an asterisk is shown
instead.
The consensus sequence is editable within Sequence Investigator. Your edited bases
will appear in lower case.