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Bioinformatics Vol. 19 Suppl. 2 2003
pages ii189-ii195
© 2003 Oxford University Press

Divide-and-conquer multiple alignment with segment-based constraints

Michael Sammeth 1,*, Burkhard Morgenstern 2 and Jens Stoye 1

1 Bielefeld University, Department of Genome Informatics, Technical Faculty, P.O. 10 01 31, 33594 Bielefeld, Germany
2 University of Göttingen, Department of Bioinformatics, Institute of Microbiology and Genetics, Goldschmidtstr. 1, 37077 Göttingen, Germany

Received on March 17, 2003 ; accepted on June 9, 2003

A large number of methods for multiple sequence alignment are currenty available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. Global strategies can be outperformed by approaches based on local similarities and vice versa, depending on the characteristics of the input sequences. In recent years, mixed approaches that include both global and local features have shown promising results. Herein, we introduce a new algorithm for multiple sequence alignment that integrates the global divide-and-conquer approach with the local segment-based approach, thereby combining the strengths of those two strategies.

Contact: micha{at}sammeth.net

* To whom correspondence should be addressed.


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