DIALIGN: Finding local similarities by multiple sequence alignment

Motivation: DIALIGN is a new method for pairwise as Well as multiple alignment oSlzucleic acid and protein sequences. While standard alignment programs rely on comparing single residues and imposing gap penalties, DIALIGN constructs alignments by comparing whole segments of the sequences. No gap penalty is employed. This point of view is especially adequate if sequences ai-e not globally related, bur share only local similarities, as is the case in genomic DNA sequences and in many protein families. Results: Using four different data sers, we show that DIALICN is able correctly to align conserved motifs in protein sequences. Alignments produced by DIALIGN are compared systematically to the results of five other alignment programs.