While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.

The latest version of the program, DIALIGN-TX, is described in Subramanian et al. (2008), Algorithms Mol. Biol. 3:6. A web server for this program is available at Goettingen Bioinformatics Compute Server (GOBICS). A web server for multiple alignment with user-defined constraints (anchor points) as described by Morgenstern et al. (2006), Algorithms Mol. Biol. 1:6 is also available through GOBICS.

During the last few years, DIALIGN has been successfully used by many researchers to align genomic sequences; some break-through discoveries have been made based on these alignments. We set up a WWW server for multiple alignment of genomic sequences using Mike Brudno's program CHAOS and DIALIGN at GOBICS, see Brudno et al. (2004), Nuc. Acids. Res. 32:W41-W44.