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Nucleic Acids Research Advance Access originally published online on December 22, 2008
Nucleic Acids Research 2009 37(3):858-865; doi:10.1093/nar/gkn1006
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Nucleic Acids Research, 2009, Vol. 37, No. 3 858-865
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

Timo Lassmann1, Oliver Frings2 and Erik L. L. Sonnhammer1,2,*

1Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 and 2Stockholm Bioinformatics Centre, Albanova, Stockholm University, SE-10691 Stockholm, Sweden

*To whom correspondence should be addressed. Tel: +46 8 55 37 85 67; Fax: +46 8 55 37 82 14; Email: Erik.Sonnhammer{at}sbc.su.se

Received October 30, 2008. Revised November 27, 2008. Accepted December 1, 2008.

In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/).

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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G. Ostlund, T. Schmitt, K. Forslund, T. Kostler, D. N. Messina, S. Roopra, O. Frings, and E. L. L. Sonnhammer
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