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Bioinformatics Vol. 18 no. 90001 2002
Pages S312-S320
© 2002 Oxford University Press

Efficient multiple genome alignment

Michael Höhl , Stefan Kurtz and Enno Ohlebusch

Faculty of Technology, University of Bielefeld, PO Box 10 01 31, Bielefeld D-33501, Germany

Received on January 22, 2002 ; revised on March 29, 2002 ; accepted on March 29, 2002

Motivation: To allow a direct comparison of the genomic DNA sequences of sufficiently similar organisms, there is an urgent need for software tools that can align more than two genomic sequences.

Results: We developed new algorithms and a software tool ‘Multiple Genome Aligner’ (MGA for short) that efficiently computes multiple genome alignments of large, closely related DNA sequences. For example, it can align 85% percent of the complete genomes of six human adenoviruses (average length 35305 bp.) in 159 seconds. An alignment of 74% of the complete genomes of three of strains of E. coli (lengths: 5528445; 5498450; 4639221~bp.) is produced in 30 minutes.

Availability: The software MGA is available free of charge for non-commercial research institutions. For details see http://bibiserv.techfak.uni-bielefeld.de/mga/

Contact: kurtz{at}techfak.uni-bielefeld.de enno{at}techfak.uni-bielefeld.de

Keywords: genome comparison; multiple alignment; efficient algorithms; graph algorithms; suffix trees.


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