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Measuring similarities between transcription factor binding sites

Szymon M Kielbasa1*, Didier Gonze12 and Hanspeter Herzel1

Author Affiliations

1 Institute for Theoretical Biology, Humboldt University, Invalidenstraße 43, D-10115 Berlin, Germany

2 Unité de Chronobiologie Théorique, Université Libre de Bruxelles, CP 231, Campus Plaine, Bvd du Triomphe, B-1050 Bruxelles, Belgium

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BMC Bioinformatics 2005, 6:237  doi:10.1186/1471-2105-6-237

Published: 28 September 2005



Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites.


We propose to identify and group similar profiles using two independent similarity measures: χ2 distances between position frequency matrices (PFMs) and correlation coefficients between position weight matrices (PWMs) scores.


We show that these measures complement each other and allow to associate Jaspar and Transfac matrices. Clusters of highly similar matrices are identified and can be used to optimise the search for regulatory elements. Moreover, the application of the measures is illustrated by assigning E-box matrices of a SELEX experiment and of experimentally characterised binding sites of circadian clock genes to the Myc-Max cluster.