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Reference Traces

References traces are used by the automatic mutation detection programs tracediff (see section Trace Difference) and hetscan (see section Heterozygote Scanner), , and by the trace difference display in the gap4 editor(see section Editing in gap4). Ideally forward and reverse reference traces should be available and should be obtained using the same primers and sequencing chemistry as the patient data. From the "settings" menu of the editor the trace display can be set to "Auto-Diff traces". Once this is activated, whenever the user double clicks on a base in the editor sequence display, not only is the reading's trace displayed, but also its designated reference trace plus the difference between them. If its complementary reading is available, its trace and reference trace and their differences are also displayed. These trace displays and the editing cursor scroll in synch.

(Click for full size image)

Top and bottom strand differences for a heterozygous base.

The preferred way of assigning reference traces to readings is by use of "naming conventions"; that is to have a simple set of rules which control the names given to the trace files. It can be seen in the figures showing the editor that forward and reverse readings from the same patient have names with a common root but which end either F or R. This both ties the two together (so the software knows which is the corresponding complementary trace when the user double clicks on a reading) and also enables the association of readings and their reference traces. Once a convention has been adopted the rules can be defined for pregap4 by loading them via the "Load Naming Scheme" option in its File menu (see section Pregap4 Naming Schemes). For any batch of readings the reference traces are defined within pregap4's "Reference Traces" module. Note that this mode of operation, by allowing the specification of only one forward and one reverse trace, limits each batch of traces processed to those which correspond to a given pair of reference traces. The size of the batch is unlimited.

The alternative way of specifying the reference traces is to right click on their names in the editor. This also allows positive trace controls to be specified (which is not possible in pregap4).

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This page is maintained by staden-package. Last generated on 22 October 2002.