ABI Trace Import Format

Reads in lane data from file produced by ABI's GeneScan. It has been tested with an ABI 377 and GeneScan 2.1 GeneScan is a registered tradmark of Perkin-Elmir. It is likely that it will also work with the ABI 373, but it will not work with GeneScan 2.01.

The program will use this feature to read in the trace files, which are obtained by extracting lanes from a gel. However, the program expects color seperation to have been performed on the lane, so that must be done to the extracted lane. Also, the program relies on the ABI software to label the peaks in the size standard. Not only must this be done, but it must be done correctly. It is a good idea to check at least a couple of lanes from a gel to make sure that the software did indeed find the correct size standard peaks. Normally, all of this is done be default. Hint: the files have names in the form 01-sample_name, 02-sample_name, etc.

The following information will be read from the file:

• the data trace, after color seperation
• the name of the sample
• the name of the gel it was run on
• the number of the lane on the original gel
• the color of the lane size standard
• the peaks, as called by the ABI software, of the size standard.

The program will display three options for importing the file. They are:

1. Data Color
2. Size Function to use
3. Size Standard to use

The program can import either one color, or all of the colors in a lane. It is recommended that data be imported such that data from samples to compare are located next to eachother.

The sizing function is used to size the lane. When the gel is displayed by the program, it is dispalyed by size. The sizing function determines how the scan number is converted into a size in base pairs. See the "Lane Sizing Formulas" heading in the Program Featues for more information on sizing functions.

The final parameter is the size standard definition. It is used to tell which of the peaks in the size standard color from the ABI file actually belong to the size standard. For example, the ABI software might call the following peak sizes: 50.0, 56.8, 62.3, 75.0 82.1, ... Only 50.0 and 75.0 are real peaks in the size standard, so only they should be used to size the lane. Size standards can be added or modified by editing the file "standards.cfg" in the program directory. The format of that file is described in the file itself.