One of the remarkable findings of the human genome sequencing project was the discovery that coding regions account for only 5% of the genome (Venter et al. 2001) . The remaining sequence consists of repetitive DNA ($40-45%) and extensive non-coding regions for which there is very little functional information. It is within these regions that significant regulatory information presumably is concealed. The major challenge in the postgenomic age is uncovering important functional regions within this non-coding DNA. The rapid development of sequence analysis software tools, increasing availability of genomic data, and recognition of the importance of comparing data from diverse organisms are allowing scientists to make fruitful inroads to understanding genomic structure and gene expression regulation. A brief summary of software tools that are valuable for identifying regulatory information from crossspecies comparative analyses follows.