The present invention relates generally to the field of genomics. More particularly, the present invention relates to a method for gene identification beginning with user-selected input phenotypes. The method is referred to generally as the ValiGeneSM Gene Identification method, or the VGIDSM method. When more than two source populations of nucleic acids are simultaneously compared, the method may be referred to as multiplex VGIDSM. The method employs nucleic acid mismatch binding protein chromatography to effect a molecular comparison of one phenotype with others. Genes are identified as having a specified function, or as causing or contributing to the cause or pathogenesis of a specified disease, or as associated with a specific phenotype, by virtue of their selection by the method. Identified genes may be used in development of reagents, drugs and/or combinations thereof useful in clinical or other settings for prognosis, diagnosis and/or treatment of diseases, disorders and/or conditions. The method is equally suited for gene identification for agricultural, bio-engineering, medical, veterinary, and many other applications.