There has been steady progress in the computational analysis of transcription control regions, but current methods of predicting the gene regulatory features of noncoding sequences are still not accurate enough to be useful in automatic genome annotation. Therefore, detailed information on the expression patterns of newly sequenced genes is more likely to come from microarray-based high-throughput mRNA quantitation technologies, which have made revolutionary progress over the past few years and are now ready for genome-wide application. Future solutions to the regulatory element prediction problem may be found by the combined analysis of genome sequence and expression data.