An estimated 5-7% of the human genome is under selection and thus considered to be of functional importance. Protein-coding genes span only 1-2% of the human genome, leaving a considerable portion of functionally important, but often poorly characterized genomic regions. In addition to numerous, but very short regulatory sites, these regions contain conserved non-coding (CNC) sequences, and probably a large amount of non-protein coding RNA (ncRNA) genes. Many of these ncRNAs fold into stable secondary structures, which are indispensable for their function and therefore evolutionary conserved. Based on sequence and structure conservation, I have developed methods to study conserved and stable RNA secondary structures in animal and virus genomes.