ABI Trace File Export

ABI Genetic Analyzer 3100 and 3730 is a fluorescent based DNA analysis system utilizing capillary electrophoresis. The instrument is capable of running sequence and fragment analyses. It offers continuous, unattended operation with automated polymer loading, sample injection, separation and detection, and data analysis. the use of capillary electrophoresis for DNA analysis offers several significant performance advantages. With more efficient heat dissipation than slab gels, capillaries permit higher run voltage, resulting in faster run times. In addition, capillary electrophoresis enables the use of electrokinetic injection to load samples into the capillaries. The most dramatic advantage of capillary electrophoresis, however, is the elimination of manual operations that result in increased run-to-run consistency and reliability. Samples are simultaneously injected into the parallel 16/32 capillary array in, typically, less than 30 seconds. Samples information, including plate name and sample-well location, is automatically imported into the 3100/3730 system software. After each, several trace files are generated and ready for further analysis.

Trace file (or chromatograms) generated from the ABI instruments contain an array of digitized data and are one of several file types that share a common structured called the ABIF tagged data format. The general architecture of the trace files are remarkably similar to that of generated by different ABI instruments. These files contain various tagged data structures, each of which is identified by a unique primary key called a flag. Without any knowledge on the meaning of the flags, it is virtually impossible to decipher the corresponding records. Most implementations of tagged data format have a serious drawback in that when data elements are inserted or removed, the entire file must be reorganized and rewritten. In addition, the tagged structure of the sample files can seem cryptic at the first glance. This project implements the algorithm that exports the trace files generated from Applied Biosystems (ABI) Genetic Analyzer 3100 and 3730 to the comma separated value (CSV) format.