Figure 4

Gibbs Recursive Sampler analysis of the DSE regions. Typical results are shown from Gibbs Recursive Sampler [30] analysis of the organism-specific downstream sequence sets. The sequence content and positioning distribution of the motifs are represented by Sequence Logos [32] and line plots, respectively. The analysis allowed patterns to grow up to 10 nt in length, however the resulting patterns were consistently hexamers or heptamers, as shown. Positioning distributions were extracted from the output file and displayed graphically with a custom perl script. Elements 1, 2, and 3 are represented in the line plot as red, green, and blue lines, respectively. Full parameter lists for the analysis are described in Methods.