Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequili

Background: The discovery of cis-regulatory motifs still remains a challenging task even though the number of sequenced genomes is constantly growing. Computational analyses using pattern search algorithms have been valuable in phylogenetic footprinting approaches as have expression profile experiments to predict co-occurring motifs. Surprisingly little is known about the nature of cis-regulatory element (CRE) distribution in promoters. Results: In this paper we used the Motif Mapper open-source collection of visual basic scripts for the analysis of motifs in any aligned set of DNA sequences. We focused on promoter motif distribution curves to identify positional over-representation of DNA motifs. Using differentially aligned datasets from the model species Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Saccharomyces cerevisiae, we convincingly demonstrated the importance of the position and orientation for motif discovery. Analysis with known CREs and all p...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Kenneth W. Berendzen, Kurt Stüber, Klaus Harter, Dierk Wanke
• Keywords: BMCBI 2006, Motif Distribution, Promoter, Promoter Motifs