Identification of specific functional sequences through the generation of deletion constructs is limited in the sequence size that can be analyzed and is restricted to examination of single genes. Transfection of cells with reporter constructs containing putative proximal promoters may elicit strong activation when treated with receptor-specific ligands in culture, while in vivo studies may yield inconsistent results, suggesting that these receptors and transcription factors are a subset of a larger complex of regulators of gene expression. Techniques such as DNASE I hypersensitivity studies and gel shifts are excellent methods for testing functionality of putative regulatory elements; however, they are not efficient for screening candidate sequences. By contrast, computational analyses allow the examination of a significantly larger region when predicting conserved regulatory regions and signals. Computational techniques lend themselves to the identification of patterns or clusters of regulatory motifs and prediction of coregulated genes, and generate targeted predictions of candidate regulatory sequences and signaling molecules that can then be directly tested in functional and mutagenesis studies (Hughes et al. 2000; Loots et al. 2000; Pennacchio and Rubin 2003; Ovcharenko et al. 2005) .