Abstract: A system and methods for identifying sequence diversity in a gene or expressed sequence is disclosed wherein hybridization differences arising from polymorphic bases in analogous expressed sequences are identified between two or more nucleotide populations. By scaling the hybridization data to account for differences in abundance and observed intensity, sequence diversity can be identified in a highly specific and sensitive manner. Data confidence levels are also accounted for to increase the accuracy of the sequence diversity determination. The invention can be applied to both newly collected gene expression data and archived data to generate valuable insight into polymorphic behavior within complex nucleotide populations.