D64 Nucleic Acids Research, 2006, Vol. 34, Database issue two orthologous vertebrate promoters. The sites and the promoter sequences have been manually curated to ensure data consistency. The compiled data are suitable for training both classical pattern discovery programs and new emerging comparative methods. Flat ﬁles accomplishing the GFF standard format were used to store and query the information. The GenBank accession number of the sequences in each bibliographical reference was utilized to retrieve the promot- ers. Such sequences were mapped on to the corresponding RefSeq annotations to ensure we were retrieving the actual promoter. The DBTSS database (10) was ﬁnally used to reﬁne the annotation of the TSSs. Since it is the region in which most experimental studies have been focused on, we considered the sequence 500 bp immediately upstream the annotated TSS, as the promoter region in this ﬁrst release. For each annotated promoter, we only included experiment- ally tested sites in this proximal region whose motifs were correctly identiﬁed in at least two species, i.e. orthologous sites. Every known binding site was mapped on to the cor- responding promoter sequence by BLASTN (11). Those matches that exhibited <80% of identity between the sequence of the original site and the mapped motif in the promoter region were rejected. We computed BLASTN (11), CLUSTALW (12), AVID (13) and LAGAN (14) alignments of the orthologous promoters Figure 1. Examples of the ABS data retrieval system showing the annotation of a gene, the set of binding motifs from a given TF in human and mouse and the extraction of the promoter sequences containing such annotations.