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Algorithm Argos
Argos is the first successful attempt to predict regulatory modules using only the genome without training data.
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 evaluated the results of Argos for the the modules in additional File 1. Log probability scores > 70 were taken as significant, since they are found very rarely using randomized noncoding sequence 1. With this threshold and at least l00 bp overlap, half of the modules were recovered, indicating a 50% false negative rate.
Argos: prediction of regulatory modules from raw genomic sequence