DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
BACKGROUND
The performance and time complexity of an improved version of the segment-to-segment approach to multiple sequence alignment is discussed. In this approach, alignments are composed from gap-free segment pairs, and the score of an alignment is defined as the sum of so-called weights of these segment pairs.


RESULTS
A modification of the weight function used in the original version of the alignment program DIALIGN has two important advantages: it can be applied to both globally and locally related sequence sets, and the running time of the program is considerably improved. The time complexity of the algorithm is discussed theoretically, and the program running time is reported for various test examples.


BACKGROUND
The program is available on-line at the Bielefeld University Bioinformatics Server (BiBiServ) http://bibiserv.TechFak.Uni-Bielefeld.DE/dial ign/
Morgenstern
B
B
GSF - National Research Center for Environment and Health, Institute of Biomathematics and Biometry, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany. burkhard.morgenstern@rp-rorer.co.uk
D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D017386:Sequence Homology, Amino Acid; D012984:Software
D011506:Proteins