Method

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 Marchal^1,3

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

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

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

author email corresponding author email

Genome Biology 2005, 6:R113doi:10.1186/gb-2005-6-13-r113

Published:	30 December 2005

Subject areas: Bioinformatics, Genome studies, Evolution

Abstract

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.