A novel approach to identifying regulatory motifs in distantly related genomes
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
Genome Biology 2005, 6:R113 doi:10.1186/gb-2005-6-13-r113Published: 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.