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DAx Data Acquisition and Data Analysis

Using DAx as Trace Analysis software for SSR / AFLP / RAPD / CAPS

  DAx can be used to read and analyse trace files such as the files that are created by the Amersham MegaBACE™ and ABI Genescan® systems. Also supported are Staden SCF files.

The MegaBACE™ and ABI systems, like other DNA analysis systems, simultaneously detect four or five fluorescent dyes in a single capillary.
This allows for a DNA size standard, labeled with a secondary colour fluorescent dye, to be added to the sample prior to electrophoresis. The standard can be used to size the unknown DNA by comparing migration times with the known fragment sizes of the added standard.
The Automatic Trace Calibration algorithm in DAx makes setting up the recognition of the sizing standard trivial, and gives extremely good results.

calibrated colour view of 11 data files, with 3 traces in each file displayed (ROX - red, FAM - green, and HEX - blue)

When performing AFLP and other DNA sizing analyses, it is often desirable to compare the expressed fragments sizes between dozens of samples. DAx can do this using a binning sheet. Binning sheets can be automatically accumulated for up to hundreds of files being analysed.
DAx is now able to export PAUP & PHYLIP files from binning sheets.
A further recent addition is the binning map, in which each bin is represented as a coloured dot. The colour of the dot corresponds to the extent of expression in each bin.

To accomodate the high throughput nature of trace analyses, DAx has the ability to perform batch analyses, of up to thousands of files per day.

For SSR analyses, users will appreciate the peak database features, enabling recognition of components based on their BP size (or any number of alternate parameters).

Steps involved in setting up an analysis

In order to set up the analysis of unknown samples using a known fragment size calibration, the following steps are used.
  • Set up the ATC algorithm. This is done by entering a list of fragment sizes, two or three helper parameters, and identifying the calibration trace.
  • DAx is told to automatically derive a size calibration from the calibration trace.
A detailed manual on this process, including example files, can be downloaded here.