DIALIGN - FINDING LOCAL SIMILARITIES BY MULTIPLE SEQUENCE ALIGNMENT

Motivation: DIALIGN is a new method for pairwise as Well as multiple a lignment oSlzucleic acid and protein sequences. While standard alignme nt programs rely on comparing single residues and imposing gap penalti es, DIALIGN constructs alignments by comparing whole segments of the s equences. 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 pro tein families. Results: Using four different data sers, we show that D IALICN is able correctly to align conserved motifs in protein sequence s. Alignments produced by DIALIGN are compared systematically to the r esults of five other alignment programs.