with the increasing number of eukaryotic genomes available high throughput automated tools for identification of regulatory dna sequences are becoming increasingly feasible several computational approaches for the prediction of regulatory elements were recently developed here we combine the prediction of clusters of binding sites for transcription factors with context information taken from genome annotations target explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors it was specifically designed for the well annotated drosophila melanogaster genome but most options can be used for sequences from other genomes as well target explorer is available at http trantor bioc columbia edu target explorer.