Figure 6
The comparative genomics-based regulon prediction framework used. (a) Reference genome selection and data retrieval, operons of the target and reference genome can be retrieved or predicted by proper tools. (b) Orthology identification for genes in the target genome. Relatively all of the genes in the target genome should have orthology among reference genomes to make phylogenetic footprinting feasible. Operons from target and reference genome sharing at least one orthologous gene is designated as an orthologous operon. The promoter sequence of these operons are used for motif finding (c). Phylogenetic foot printing’s final step is to find DNA cis-regulatory motifs (d). Similarity score calculation (co-regulation score: see text) based on which interactions between motifs of operons were made (e). Regulons prediction by clustering the resulting network, each cluster is a regulon.
