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

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Appendix B Advanced Topic: Data Analysis Overview
Fundamentals of color-space analysis
Color-coding process
Figure 1 SOLiD 4 System’s 2-base color-coding scheme
The column under code i (0, 1, 2, or 3) lists the corresponding dye
and the di-base probes (adjacent nucleotides) encoded by color i. For
example, GT is labeled with Cy3 ® dye and coded as “1”.
The instrument takes the following steps to encode a DNA sequence.
Consider the example ATCAAGCCTC:
1. Start at the 5′ end.
2. Replace the di-base AT at this position with its corresponding
code 3 from the table.
3. Advance by one base, which shows the TC di-base (code 2).
4. Continue to advance by one base, as shown below.
This process encodes a k-mer of bases as a (k-1)-mer of colors.
Although this color string codes for four different k-mers, knowledge
of the type and position of any of its k bases helps to encode the
sequence. For SOLiD 4 System sequencing applications, the
138 Applied Biosystems SOLiD 4 System SETS Software User Guide