Massive amounts of DNA sequence data, generated from expressed sequence tag (EST) and genome sequencing projects, require efficient methods to link sequence databases with temporal and spatial expression profiles. To meet this need, we have developed a powerful computer program (GenEST), which links cDNA sequence data (including EST sequences) with transcript profiles revealed by cDNA-amplified fragment length polymorphism (AFLP). cDNA-AFLP is a highly reproducible differential display method based on restriction enzyme digests and selective amplification under high stringency conditions. GenEST predicts the sizes of virtual transcript derived fragments (TDFs) from cDNA sequences digested in silico. The resulting virtual TDFs could be traced back among the thousands of TDFs displayed on cDNA-AFLP gels. As a consequence, cDNA sequence databases can be screened very efficiently to identify genes with relevant expression profiles. Vice versa, using the restriction enzyme recognition sites, the primer extensions and the estimated TDF size as identifiers, the DNA sequence(s) corresponding to a TDF with an interesting expression pattern can be identified.