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Bioinformatics Vol. 16 no. 10 2000
Pages 948-949
© 2000 Oxford University Press

Applications Note

A space-efficient algorithm for aligning large genomic sequences

Burkhard Morgenstern 1,2

1 MIPS–Max-Planck-Institut für Biochemic, Am Klopferspitz 18a, 82152 Martinsried, Germany
2 Aventis Pharma Limited, Rainham Road South, Essex RM10 7XS, UK

Received on March 23, 2000 ; revised on June 5, 2000 ; accepted on June 5, 2000

Summary: In the segment-by-segment approach to sequence alignment, pairwise and multiple alignments are generated by comparing gap-free segments of the sequences under study. This method is particularly efficient in detecting local homologies, and it has been used to identify functional regions in large genomic sequences. Herein, an algorithm is outlined that calculates optimal pairwise segment-by-segment alignments in essentially linear space.

Availability: The program is available at the Bielefeld Bioinformatics Server (BiBiServ) at http://bibiserv.techfak.uni-bielefeld.de/dialign/

Contact: morgenstern{at}mips.biochem.mpg.de


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