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Motivation: The process of transcription is controlled by systems of factors which bind in specific arrangements, called cis-regulatory modules (CRMs), in promoter regions. We present a discriminative learning algorithm which simultaneously learns the DNA binding site motifs as well as the logical structure and spatial aspects of CRMs.Results: Our results on yeast datasets show better predictive accuracy than a current state-of-the-art approach on the same datasets. Our results on yeast, fly and human datasets show that the inclusion of logical and spatial aspects improves the predictive accuracy of our learned models.Availability: Source code is available at http://www.cs.wisc.edu/~noto/crmContact:noto@cs.wisc.edu [ABSTRACT FROM AUTHOR]