Sequence conservation has traditionally been used as a means to target 
functional regions of complex genomes. In addition to its use in identifying 
coding regions of genes, the recent availability of whole genome data for a 
number of vertebrates has permitted high-resolution analyses of the noncoding 
"dark matter" of the genome. This has resulted in the identification of a large 
number of highly conserved sequence elements that appear to be preserved in all 
bony vertebrates. Further positional analysis of these conserved noncoding 
elements (CNEs) in the genome demonstrates that they cluster around genes 
involved in developmental regulation. This chapter describes the identification 
and characterization of these elements, with particular reference to their 
composition and organization.