Comparative genomics is the direct comparison of large amounts of genetic material of one organism against that of another. It is a new and rapidly developing field of biology with numerous beneficial applications, both within and outside the biomedical sciences. The highly publicized successful analysis of the human genome is but the most visible of many initiatives. Other national and international efforts are directed at completing the genomic sequences of a variety of model organisms. Comparative studies may involve testing the genomes of pathogens against closely related non-pathogenic species, the contrast of crop plant genomes against those of model plant species, and the analysis of the genomes of individuals with genetic diseases against healthy individuals. Such analyses allow the identification of genes and permits inferences about gene function. This will yield unique insights into the relationships among organisms and between an organism and its environment.

Genomics represents a new conceptual approach to the study of biology. It uses the rapid generation of huge quantities of precise DNA sequence data to identify genes, the structures of genes, and other elements in a genome. The functions of these genes can further be assessed by a number of high-throughput approaches called "functional genomics". Using genomics based approaches, it is possible to identify genes that determine complex character traits in very large populations, characterize the expression patterns of every gene within a species under all possible circumstances, and therefore ultimately shed light on questions as diverse as the origins of the nervous system, the development of organisms from the single cell egg, and the mechanisms underlying disease. Genomics lays the foundation for the use of recombinant DNA technology, so-called reverse genetics, to determine the effect on the organism of mutations in all of the genes within a species. The ultimate goal of genomics is to find every gene and to determine the roles of each of these genes. Comparative genomics takes this goal several steps further: to identify and find the role of every gene in every species, to see what changes are significant in making one species different (in phenotype, growth habit, adapted environment) from another, and to determine how these changes came about.