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Nucleic Acids Research 2006 34(Web Server issue):W110-W115; doi:10.1093/nar/gkl203
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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

TreeDet: a web server to explore sequence space

Angel Carro, Michael Tress, David de Juan, Florencio Pazos, Pedro Lopez-Romero1, Antonio del Sol2, Alfonso Valencia and Ana M. Rojas*

Protein Design Group, CNB-CSIC C/Darwin n.3 28049, Madrid, Spain 1 Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid, Spain 2 Bioinformatics Research Project, Fujirebio Inc. Tokyo, Japan

*To whom correspondence should be addressed at Spanish National Cancer Center (CNIO), Structural Bioinformatics Group, Centro Nacional de Investigaciones Oncológicas (CNIO), C/Melchor Fernandez Almagro 3, 28029 Madrid, Spain. Tel: +34 91 585 46 69; Fax: +34 91 585 45 06; Email: arojas{at}cnb.uam.es

Received February 10, 2006. Revised March 22, 2006. Accepted March 22, 2006.

The TreeDet (Tree Determinant) Server is the first release of a system designed to integrate results from methods that predict functional sites in protein families. These methods take into account the relation between sequence conservation and evolutionary importance. TreeDet fully analyses the space of protein sequences in either user-uploaded or automatically generated multiple sequence alignments. The methods implemented in the server represent three main classes of methods for the detection of family-dependent conserved positions, a tree-based method, a correlation based method and a method that employs a principal component analyses coupled to a cluster algorithm. An additional method is provided to highlight the reliability of the position in the alignments. The server is available at http://www.pdg.cnb.uam.es/servers/treedet.


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[Abstract] [Full Text] [PDF]


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