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A novel approach to identifying regulatory motifs in distantly related genomes

Ruth Van Hellemont1, Pieter Monsieurs1, Gert Thijs1, Bart De Moor1, Yves Van de Peer2 and Kathleen Marchal13*

Author Affiliations

1 ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium

2 Plant Systems Biology, Bioinformatics and Evolutionary Genomics, VIB/Ghent University, Technologiepark 927, 9052 Gent, Belgium

3 Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven-Heverlee, Belgium

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Genome Biology 2005, 6:R113  doi:10.1186/gb-2005-6-13-r113

Published: 30 December 2005


Although proven successful in the identification of regulatory motifs, phylogenetic footprinting methods still show some shortcomings. To assess these difficulties, most apparent when applying phylogenetic footprinting to distantly related organisms, we developed a two-step procedure that combines the advantages of sequence alignment and motif detection approaches. The results on well-studied benchmark datasets indicate that the presented method outperforms other methods when the sequences become either too long or too heterogeneous in size.