TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes : comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes. It is a platform independent, standalone Java application that is tightly linked with Ensembl, and was built using the BioJava package. SOAP web services are used to remotely access multiple algorithms for comparative genomics, motif detection, and module detection.