7. GS Run Browser Appendices
: 7.1 Control DNA Keys and Sequences for the Different Chemistries
7.1
Control DNA Keys and Sequences for the Different Chemistries
The 454 Sequencing System software is fully backward-compatible and can process data sets generated with any implementation of the system, including the current GS Junior Titanium and GS FLX Titanium chemistry, the GS FLX standard chemistry, and the now retired GS 20 version of the system. One of the features that changed between the main versions of the system is the Control DNA sequences provided in the form of Control DNA Beads in the Sequencing kits. This section describes the differences between the various sets of Control DNA test fragments. These differences affect the number, key, sequence and length of the Control DNA sequences.
Two different sequencing Control DNA keys are used in the GS Junior Titanium and GS FLX Titanium chemistry:
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CATG (Type I): A set of six long Control DNA sequences (the AvTF series) carry this key.
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ATGC (Type II): Type II Control DNA Beads carry longer test fragments than the Type I beads. This set consists of four additional Control DNA sequences (the EcTF series) that are designed such that at least one of them will generate signal at every nucleotide flow of a sequencing Run. Use of Type II Control DNA Beads is important when sequencing Amplicon libraries in the GS Junior Titanium and GS FLX Titanium chemistry.
Past chemistries, the GS 20 and GS FLX standard chemistries, also use the ATGC key. In these cases, however, the test fragments are shorter (the BHTF series) and do not have the special “signal at every flow” feature of the Type II beads. They are thus considered Type I.
The 454 Sequencing System software (data processing algorithms, GS Run Browser, etc.) are aware of these different kinds of Control DNA Beads and handle / report them appropriately.
