We describe here the GeneCalling� method for the discovery of differentially expressed genes, both known and novel, from any species and with useful sequence information to determine the potential function of novel genes captured. The method relies on transcript visualization coupled to a database query to rapidly and quantitatively identify differentially expressed transcripts. The method has been applied to a wide variety of disease models in a wide variety of species, addressing problems as diverse as identifying novel human cancer gene targets, understanding how drugs and diet affect animal models of disease, and understanding the basis of trait differences in related strains of corn.