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CORECLUST uses an HMM-based technique to predict cis-regulatory modules (CRMs) given known motifs for a set of system-specific transcription factors (TFs). Given regulatory regions of orthologous and/or co-regulated genes, CORECLUST constructs a model describing conserved rules of relative location of TF binding sites (CRM structure). The constructed model may be used for the CRM prediction, as well as for the investigation of the regulatory grammar of the system of interest.
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