Tool for finding evolutionarily conserved mammalian enhancer elements. For description of the underlying alignment algorithm, see Hallikas et.al. 2006
Some user guidance is available at [http://www.cs.helsinki.fi/u/kpalin/EEL/] or in Palin et.al. 2006
If you use EEL in academic publications, please cite:
Hallikas, Palin,Sinjushina, Rautiainen, Partanen Ukkonen, Taipale: Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription Factor Binding Affinity. CELL 124, January 13, 2006.
Copyright Kimmo.Palin at helsinki.fi Licence GPL
Newer versions of EEL contain a new command "computeKLdistances" which computes all pairwise comparisons of loaded TF binding motifs. The "help" command will explain the syntax. The method is used and described in Wei et.al. 2010. If you use this method in academic publications, please cite:
Wei, G. H., Badis, G., Berger, M. F., Kivioja, T., Palin, K., Enge, M., ... & Taipale, J. (2010). Genome‐wide analysis of ETS‐family DNA‐binding in vitro and in vivo. The EMBO journal, 29(13), 2147-2160.
The article describes the method by:
Comparison of binding profiles was performed using a novel algorithm that determines the similarity between TF motifs using the minimum Kullback–Leibler divergence between all translations and reverse complementations of the multinomial distributions defined by the motifs. Conceptually, the TF-motif divergence measures the information gained about the DNA sequence by knowledge of having binding sites for both of the two factors. The TF-motif divergence is defined as the minimum Kullback–Leibler divergence between all translations and reverse complementations of the multinomial distributions defined by the two TF motifs. The longer motif is inserted to a sequence with background distribution and the shorter motif is slid over the background/longer motif sequence. The KL divergence is computed between the multinomial distributions defined by (1) the shorter motif and (2) the part of the background/longer motif sequence overlapping the shorter motif. The same is repeated with the background/long motif sequence reverse complemented and the minimum of the KL divergences is taken. The TF-motif divergence is symmetric but does not fulfill the triangle inequality and thus is not a metric in the mathematical sense.