DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment Stoye, Jens; Moulton, Vincent; Dress, Andreas W. M.
Suggested Citation Stoye, Jens ; Moulton, Vincent ; Dress, Andreas W. M. (1997) DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Computer applications in the biosciences, 13(6), pp. 625-626 Posted at BiPrints Repository, Bielefeld University. http://repositories.ub.uni-bielefeld.de/biprints/volltexte/2006/58
DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment Abstract DCA is a new computer program for multiple sequence alignment which utilizes a 'devide-and-conquer' type of heuristic approach.
Vol. 13 no. 6 1997
CABIOS
Pages 625-626
DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment Jens Stoye, Vincent Moulton and Andreas W.M. Dress Research Center for Interdisciplinary Studies on Structure Formation {FSPM), University of Bielefeld, Postfach 100 131, 33501 Bielefeld, Germany Received on July 7, 1997, revised and accepted on July 31, 1997
Abstract Motivation: DCA is a new computer program for multiple sequence alignment which utilizes a 'divide-and-conquer' type of heuristic approach. Availability: The algorithm is freely available from http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/ Contact: E-mail:
[email protected] We present a new computer program, DCA, for the multiple alignment of DNA, RNA and protein sequences. Utilizing a divide-and-conquer type heuristic (cf. Brinkmann et at., 1997), it aims to produce multiple alignments which minimize the sum-of-pairs alignment score. Consequently, and in contrast to most other multiple sequence alignment programs currently in use which construct alignments by progressively aligning alignments of alignments of alignments (see, for instance, Barton and Steinberg, 1987; Thompson et al., 1994; Gotoh, 1995; Feng and Doolittle, 1996), DCA processes any given sequence family simultaneously, already taking all sequences into consideration at its first alignment step. The algorithm is based on the following observation. Given a score-optimal alignment A - (ci,j)\
