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Nucleic Acids Research 2006 34(Web Server issue):W596-W599; doi:10.1093/nar/gkl191
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment

Timo Lassmann* and Erik L. L. Sonnhammer

Center for Genomics and Bioinformatics, Karolinska Institutet S-17177 Stockholm, Sweden

*To whom correspondence should be addressed. Tel: +46 0 8 5248 6372; Fax: +46 0 8 337983; Email: timo.lassmann{at}ki.se

Received February 13, 2006. Accepted February 20, 2006.

Obtaining high quality multiple alignments is crucial for a range of sequence analysis tasks. A common strategy is to align the sequences several times, varying the program or parameters until the best alignment according to manual inspection by human experts is found. Ideally, this should be assisted by an automatic assessment of the alignment quality. Our web-site http://msa.cgb.ki.se allows users to perform all these steps: Kalign to align sequences, Kalignvu to view and verify the resulting alignments and Mumsa to assess the quality. Due to the computational efficiency of Kalign we can allow users to submit hundreds of sequences to be aligned and still guarantee fast response times. All servers are freely accessible and the underlying software can be freely downloaded for local use.


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