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Its entire output can then be used as input to Ahab (Figure 1).
Using only three modules as input, Ahab finds 63 significant modules in the genome
Using these 6 weight matrices as input, Ahab finds 63 highly significant modules genome-wide (Table 4, additional File 5).
Namely, following the hierarchical structure in Figure 1, Argos could be used to predict modules, then the customized Gibbs sampler to predict binding sites (weight matrices) and finally Ahab to predict, genome wide, genes in the same regulatory network.
We also varied the window size to 700 bp and masked out the repeats genome wide, before running Ahab, (see web site).