Nucleic Acids Research, 2006, Vol. 34, Web Server issue W527 welcome any requests for new motifs to be added. The default method of obtaining results ﬁles is via email. However, if there is a desire for anonymity then an alternative method allows the user to manually check whether a job has ﬁnished by following a web page link that is provided when the job is submitted (without the need to enter an email address). If the link is followed before the job is ﬁnished, a message to that effect is displayed. This page will refresh every 30 s until the job is completed. Either the results will be displayed or a message stating that no clusters were found. Throughout, all user input screens are designed to be simple and used in a step-wise manner; appropriate default values have been pre-entered as good starting points to run the analysis. CONCLUSIONS Modern biology is increasingly dependent on computational infrastructure to integrate diverse datasets from multiple different organisms and of multiple different types. TFBScluster is designed to utilize diverse information (e.g. genome annotation, comparative genomics and expression proﬁling) to permit the formulation of novel experimentally testable propositions about the likely biological function of gene regulatory elements. Understanding the function of tran- scriptional regulatory elements represents a critical step in our ability to reconstruct transcriptional regulatory networks. TFBScluster is therefore potentially widely applicable for future studies of human and murine developmental systems and disease models. Moreover, TFBScluster could be readily adaptable for other genomes annotated in Ensembl. ACKNOWLEDGEMENTS Work in the authors’ laboratory is funded by the Cambridge MIT Institute, an SUR grant from IBM and the Leukaemia Research Fund. 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