Nucleic Acids Research Advance Access originally published online on October 23, 2008
Nucleic Acids Research 2009 37(Database issue):D261-D266; doi:10.1093/nar/gkn680
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Nucleic Acids Research, 2009, Vol. 37, Database issue D261-D266
© 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.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
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PeroxiBase: a database with new tools for peroxidase family classification
1Swiss Institute of Bioinformatics, Swiss-Prot Group, CMU, 1 rue Michel Servet, 2Laboratory of Plant Physiology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4 and 3Swiss Institute of Bioinformatics, EMBnet Group, Quartier Sorge - Bâtiment Génopode, CH-1015 Lausanne, Switzerland
*To whom correspondence should be addressed. Tel: 0033 562 193 557; Fax: 0033 562 193 502; Email: dunand{at}scsv.ups-tlse.fr
Received August 15, 2008. Revised September 19, 2008. Accepted September 23, 2008.
Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. They use various peroxides as electron acceptors to catalyse a number of oxidative reactions and are present in almost all living organisms. We have created a peroxidase database (http://peroxibase.isb-sib.ch) that contains all identified peroxidase-encoding sequences (about 6000 sequences in 940 organisms). They are distributed between 11 superfamilies and about 60 subfamilies. All the sequences have been individually annotated and checked. PeroxiBase can be consulted using six major interlink sections ‘Classes’, ‘Organisms’, ‘Cellular localisations’, ‘Inducers’, ‘Repressors’ and ‘Tissue types’. General documentation on peroxidases and PeroxiBase is accessible in the ‘Documents’ section containing ‘Introduction’, ‘Class description’, ‘Publications’ and ‘Links’. In addition to the database, we have developed a tool to classify peroxidases based on the PROSITE profile methodology. To improve their specificity and to prevent overlaps between closely related subfamilies the profiles were built using a new strategy based on the silencing of residues. This new profile construction method and its discriminatory capacity have been tested and validated using the different peroxidase families and subfamilies present in the database. The peroxidase classification tool called PeroxiScan is accessible at the following address: http://peroxibase.isb-sib.ch/peroxiscan.php.
Present address: Christophe Dunand, SCSV-UMR5546 CNRS/UPS, 24 Chemin de Borderouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
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  C. J. A. Sigrist, L. Cerutti, E. de Castro, P. S. Langendijk-Genevaux, V. Bulliard, A. Bairoch, and N. Hulo PROSITE, a protein domain database for functional characterization and annotation Nucleic Acids Res., October 25, 2009; (2009) gkp885v1. [Abstract] [Full Text] [PDF]
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