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Bioinformatics. 2005 Jul 1;21(13):3058-9. Epub 2005 Apr 26.

TFBScluster: a resource for the characterization of transcriptional regulatory networks.

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  • 1Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge Hills Road, Cambridge CB2 2XY, UK.



One major challenge of the post-sequencing era of the human genome project will be the functional annotation of the non-coding portion of the genome, in particular gene regulatory sequences. We have developed a new web-based tool, TFBScluster, which performs genome-wide identification of transcription factor binding site clusters that are conserved in multiple mammalian genomes. Clusters representing candidate gene regulatory elements can be filtered further, based on the presence or absence of additional user-defined DNA sequence motifs or by constraining the orientation or order of binding sites. Comprehensive results files, returned by email, are designed to facilitate experimental validation of computationally identified candidate gene regulatory sequences. TFBScluster, therefore, has the potential to contribute to deciphering transcriptional networks that regulate a wide range of mammalian developmental processes.

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