Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

B
Applied Biosystems SOLiD 4 System SETS Software User Guide
Appendix B
Advanced Topic: Data Analysis
Overview
The topics provided in this appendix are intended for advanced users
of the SOLiD 4 System and do not apply to the typical user.
Fundamentals of color-space analysis
The 2-base color coding scheme
The Applied Biosystems SOLiD 4 System sequencing technology
is based on sequential ligation of dye-labeled oligonucleotides. This
technology makes possible massive parallel sequencing of clonally
amplified DNA fragments. Features of this system, such as matepaired
analysis and 2-base encoding, enable studies of complex
genomes by providing a greater degree of accuracy. This section
describes the principles of 2-base encoding and the benefits of
performing analysis in the di-base alphabet, known as color-space
analysis.
Until recently, most DNA sequencing was performed using the chain
termination method developed by Frederick Sanger. (Refer to the
paper by Sanger F., Coulson A. R., 1975, A rapid method for
determining sequences in DNA by primed synthesis with DNA
polymerase. J Mol Biol. 94(3): 441-448.) This type of sequencing is
often referred to as Sanger sequencing. Sanger sequencing data is
also encoded in color-space by the four fluorescent dyes used in the
sequencing chemistry and displayed as peaks in an
electropherogram. In Sanger sequencing, each color, representing
only a single nucleotide, is automatically translated to A, C, G, or T.
With the SOLiD 4 System, each color represents four potential 2base
combinations (see Figure 1). The conversion into nucleotide
base space is usually done after the sequence is aligned to a reference
genome transcribed in color-space. As an alternative, translation can
occur following the generation of a consensus sequence.
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