Abstract: MOTIVATION: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p respectively. The binding sites for these factors share a common core CACGTG. We evaluate our capability to discriminate phosphate- and methionine-responding genes on the basis of putative regulatory elements, despite the similarity between Met4p/Met28p/Cbf1p and Pho4p consensus. RESULTS: We scanned upstream regions of methionine, phosphate and control genes with position-specific weight matrices for Pho4p, Met4p/Met28p/Cbf1p, and Met31p/Met32p, and applied discriminant analysis to classify genes according to matrix matching scores. This analysis showed that matrix scores provided a good discrimination between phosphate, methionine and control genes. The optimal parameters have then been used to predict phosphate and methionine regulation at a genome scale. Genome-scale analysis predicts 37 genes as methionine-regulated, and 40 as phosphate-regulated. We compare the predictive results with high throughput data and discuss the difference. AVAILABILITY: The programs for sequence retrieval and analysis, as well as the complete data and results, are available on the web site Regulatory Sequence Analysis Tools (http://rsat.scmbb.ulb.ac.be/rsat/) (van Helden et al., 2000; van Helden, 2003).