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Nucleic Acids Research 2006 34(Web Server issue):W604-W608; doi:10.1093/nar/gkl092
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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

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

Fabrice Armougom, Sébastien Moretti, Olivier Poirot, Stéphane Audic, Pierre Dumas1, Basile Schaeli1, Vladimir Keduas and Cedric Notredame*

Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France 1 Laboratoire de systèmes périphériques, Ecole Polytechnique Fédérale de Lausanne CH 1015 Lausanne, Switzerland

*To whom correspondence should be addressed. Tel: +33 491 825 427; Fax: +33 491 825 420; Email: cedric.notredame{at}europe.com

Received February 14, 2006. Revised March 1, 2006. Accepted March 7, 2006.

Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on http://www.tcoffee.org/.


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