The identification of promoters and their regulatory elements is one of the 
major challenges in bioinformatics and integrates comparative, structural, and 
functional genomics. Many different approaches have been developed to detect 
conserved motifs in a set of genes that are either coregulated or orthologous. 
However, although recent approaches seem promising, in general, unambiguous 
identification of regulatory elements is not straightforward. The delineation of 
promoters is even harder, due to its complex nature, and in silico promoter 
prediction is still in its infancy. Here, we review the different approaches 
that have been developed for identifying promoters and their regulatory 
elements. We discuss the detection of cis-acting regulatory elements using 
word-counting or probabilistic methods (so-called "search by signal" methods) 
and the delineation of promoters by considering both sequence content and 
structural features ("search by content" methods). As an example of search by 
content, we explored in greater detail the association of promoters with CpG 
islands. However, due to differences in sequence content, the parameters used to 
detect CpG islands in humans and other vertebrates cannot be used for plants. 
Therefore, a preliminary attempt was made to define parameters that could 
possibly define CpG and CpNpG islands in Arabidopsis, by exploring the 
compositional landscape around the transcriptional start site. To this end, a 
data set of more than 5,000 gene sequences was built, including the promoter 
region, the 5'-untranslated region, and the first introns and coding exons. 
Preliminary analysis shows that promoter location based on the detection of 
potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. 
Nevertheless, because the landscape of CpG/CpNpG islands differs considerably 
between promoters and introns on the one side and exons (whether coding or not) 
on the other, more sophisticated approaches can probably be developed for the 
successful detection of "putative" CpG and CpNpG islands in plants.