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JXB Advance Access originally published online on December 26, 2008
Journal of Experimental Botany 2009 60(2):453-459; doi:10.1093/jxb/ern317
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© The Author [2008]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

REVIEW-ARTICLE

PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae

Michele Oliva1 *, Grégory Theiler1, Marcel Zamocky2, Dominique Koua1 {dagger}, Marcia Margis-Pinheiro3, Filippo Passardi1 and Christophe Dunand4,{ddagger}

1Department of Plant Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
2Department of Chemistry, University of Natural Resources and Applied Life Sciences, Vienna, Austria
3Federal University of Rio Grande do Sul, Department of Genetics, Institute of Biology, Brazil
4Plant Cell Surfaces and Signaling Laboratory, University of Toulouse, UPS, CNRS, 24 Chemin de Borderouge, F-31326 Castanet-Tolosan, France

{ddagger} To whom correspondence should be addressed: E-mail: dunand{at}scsv.ups-tlse.fr

Peroxidases are enzymes that are implicated in several biological processes and are detected in all living organisms. The increasing number of sequencing projects and the poor quality of annotation justified the creation of an efficient tool that was suitable for collecting and annotating the huge quantity of data. Started in 2004 to collect only class III peroxidases, PeroxiBase has undergone important updates since then and, currently, the majority of peroxidase sequences from all kingdoms of life is stored in the database. In addition, the web site (http://peroxibase.isb-sib.ch) provides a series of bioinformatics tools and facilities suitable for analysing these stored sequences. In particular, the high number of isoforms in each organism makes phylogenetic studies extremely useful to elucidate the complex evolution of these enzymes, not only within the plant kingdom but also between the different kingdoms. This paper provides a general overview of PeroxiBase, focusing on its tools and the stored data. The main goal is to give researchers some guidelines to extract classified and annotated sequences from the data base in a quick and easy way in order to perform alignments and phylogenetic analysis. The description of the database is accompanied by the updates we have recently carried out in order to improve its completeness and make it more user-friendly.

Key words: Database, evolution, peroxidases, phylogenetic analyses, Viridiplantae

* Present address: BioQuant Center, Heidelberg Institute for Plant Sciences, University of Heidelberg, D-69120 Heidelberg, Germany.

{dagger} Present address: Swiss Institute of Bioinformatics, Swiss-Prot Group, CMU-1, rue Michel Servet, CH-1211 Geneva 4, Switzerland.

Received 15 August 2008; Revised 13 November 2008 Accepted 17 November 2008


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