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Bioinformatics, Vol 14, 290-294, Copyright © 1998 by Oxford University Press

ARTICLES

DIALIGN: finding local similarities by multiple sequence alignment

B Morgenstern, K Frech, A Dress and T Werner
GSF-National Research Center for Environment and Health, Institute of Biomathematics and Biometry, Institute of Mammalian Genetics, Ingolstadter Landstr. 1, 85764 Neuherberg, Germany.

MOTIVATION: DIALIGN is a new method for pairwise as well as multiple alignment of nucleic 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 are not globally related, but share only local similarities, as is the case in genomic DNA sequences and in many protein families. RESULTS: Using four different data sets, we show that DIALIGN 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. AVAILABILITY: DIALIGN is available to the scientific community free of charge for non- commercial use. Executables for various UNIX platforms including LINUX can be downloaded at http://www.gsf.de/biodv/dialign.html Contact: werner, morgenstern@gsf.de
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