Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.
Align-m—a new algorithm for multiple alignment of highly divergent sequences
1 Department of Ultrastructure, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium and 2 Algonomics NV, Technologiepark 4, 9052 Gent-Zwijnaarde, Belgium
Received on July 31, 2003; revised on December 15, 2003; accepted on December 24, 2003
Advance Access Publication February 12, 2004
Motivation: Multiple alignment of highly divergent sequences is a challenging problem for which available programs tend to show poor performance. Generally, this is due to a scoring function that does not describe biological reality accurately enough or a heuristic that cannot explore solution space efficiently enough. In this respect, we present a new program, Align-m, that uses a non-progressive local approach to guide a global alignment.
Results: Two large test sets were used that represent the entire SCOP classification and cover sequence similarities between 0 and 50% identity. Performance was compared with the publicly available algorithms ClustalW, T-Coffee and DiAlign. In general, Align-m has comparable or slightly higher accuracy in terms of correctly aligned residues, especially for distantly related sequences. Importantly, it aligns much fewer residues incorrectly, with average differences of over 15% compared with some of the other algorithms.
Availability: Align-m and the test sets are available at http://bioinformatics.vub.ac.be
Contact: ivwalle{at}vub.ac.be
* To whom correspondence should be addressed.
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