A novel approach to identifying regulatory motifs in distantly related genomes.
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.
Van Hellemont
Ruth
R
ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium. Ruth.vanhellemont@esat.kuleuven.be
Monsieurs
Pieter
P
Thijs
Gert
G
de Moor
Bart
B
Van de Peer
Yves
Y
Marchal
Kathleen
K
D000595:Amino Acid Sequence; D000818:Animals; D020029:Base Pairing / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D030541:Databases, Genetic; D005136:Eye Proteins / Q000737:chemistry; D016678:Genome / Q000235:genetics*; D018398:Homeodomain Proteins / Q000737:chemistry; D006801:Humans; D008969:Molecular Sequence Data; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors / Q000737:chemistry; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012097:Repressor Proteins / Q000737:chemistry
D005136:Eye Proteins; D018398:Homeodomain Proteins; D000071841:PAX6 Transcription Factor; C000605730:PAX6 protein, human; D051761:Paired Box Transcription Factors; D012097:Repressor Proteins