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Genome Biol. 2005;6(13):R113. Epub 2005 Dec 30.

A novel approach to identifying regulatory motifs in distantly related genomes.

Author information

  • 1ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium. Ruth.vanhellemont@esat.kuleuven.be

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.

PMID:
16420672
[PubMed - indexed for MEDLINE]
PMCID:
PMC1414112
Free PMC Article

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