from each gene. Moreover, we produced a dotplot of word matches with EMBOSS (15) to visualize unusually conserved regions. For comparative assessments, computational predic- tions using the JASPAR (5), TRANSFAC (6) and PROMO (16) collections of position weight matrices were calculated. A very restrictive threshold of 0.85 was used to remove those predicted TFBSs whose score was below this value, creating a ﬁrst group of more reliable predictions. A second group of predictions was produced using a more ﬂexible threshold of 0.70 (see the ABS website for further information about the scoring method). Nucleic Acids Research, 2006, Vol. 34, Database issue D65 DATABASE CONTENTS Release 1.0 of ABS database contains 100 annotated ortholo- gous genes, each entry corresponding to two or more species. The total number of promoter sequences is 211 (105 500 nt). There is a clear predominance of human and mouse annota- tions: 73 entries contain at least annotations for human–mouse orthologs. A total of 650 experimental binding sites from 68 different TFs are associated with ABS entries, covering 8624 nt. In average, three TFBSs per sequence have been mapped on to the promoters with an average length of 13.3 nt per site. The majority of the TFBSs are found near Figure 2. Protocol to evaluate the accuracy of an external motif-finding program on a synthetic dataset generated by planting motifs from ABS in randomly generated sequences.