The interactive program MACAW [11] can be used for semi-automatic alignment with user-defined constraints; similarly the program OWEN [12,13] accepts anchor points for pairwise alignment. Multiple-alignment methods accepting pre-defined constraints have also been proposed by Myers et al. [14] and Sammeth et al. [15]. The multi-alignment program DIALIGN [16,17] has an option that can be used to calculate alignments under user-specified constraints. Originally, this program feature has been introduced to reduce the alignment search space and program running time for large genomic sequences [18,19]; see also [20]. At Göttingen Bioinformatics Compute Server (GOBICS), we provide a user-friendly web interface where anchor points can be used to guide the multiple alignment procedure [21]. Herein, we describe our anchored-alignment approach in detail using a previously introduced set-theoretical alignment concept. We apply our method to genomic sequences of the Hox gene clusters. For these sequences, the default version of DIALIGN produces serious mis-alignments where entire genes are incorrectly aligned, but meaningful alignments can be obtained if the known gene boundaries are used as anchor points.