D262 Nucleic Acids Research, 2009, Vol. 37, Database issue peroxide, respectively). Two particular cases are also observed for numbers EC 1.11.1.2 (NADPH peroxidase) and 1.11.1.3 (fatty acid peroxidase) and no known perox- idase sequence has been assigned to NADPH peroxidase. Peroxidasins, peroxinectins, other non-animal peroxi- dases, Dyp-type peroxidases, hybrid ascorbate-cyto- chrome C peroxidases and other Class II peroxidases do not possess their own EC number and can only be classi- ﬁed in EC 1.11.1.7. At the sequence level, most haem peroxidases belong to two large families, one mainly found in plants and also in bacteria and fungi (7,8), and a second found mostly in animals (but also occasionally in some fungal and bacte- rial species) (9,10). These two independent groups, though possessing weak sequence homology, can still be identiﬁed with a common signature (see InterPro entry IPR010255). In addition to these two large superfamilies, four smaller protein families are indexed as capable of reducing per- oxide molecules with the help of haem. Catalases (Kat), which can also oxidize hydrogen peroxide (unique fea- ture); Di-haem cytochrome C peroxidases (DiHCcP); Dyp-type peroxidases (DypPrx); and haem Haloperoxi- dases (HalPrx). These families display no sequence homol- ogy between each other. Non-haem peroxidases are not evolutionarily linked and form ﬁve independent families. The largest one is the thiol peroxidase, which currently contains more than 1000 members grouped in two diﬀerent subfamilies (Glutathione peroxidases and Peroxiredoxines). Alkylhy- droperoxidase, non-haem haloperoxidase, manganese cat- alase and NADH peroxidase are the remaining other four non haem peroxidase families. According to the phylogenetic trees these 11 major groups can be subdivided in 60 subfamilies (Figure 1). These subdivisions based on evolution describe quite well the variety of peroxidase functions and can thus be used to predict the function of newly characterized proteins. Due to the high diversity of peroxidase functions and increased interest of the medical research in pathologies related to the role of peroxidases there is an urgent need to federate and organize data on peroxidases. The goal of our database is to centralize most sequences that belong to peroxidase superfamilies, to follow the evolution of peroxidase among living organism and to compile the information concerning putative functions and transcrip- tional regulation. Currently, PeroxiBase is a unique repo- sitory exclusively dedicated to peroxidase families and superfamilies from both Eukaryotes and Prokaryotes. It includes 6000 peroxidases encoding sequences from 940 organisms, and each sequence is individually annotated. We have also developed a new tool to facilitate the classi- ﬁcation of new peroxidase members. DATABASE INTERFACE ORGANIZATION The PeroxiBase toolbar is divided into eight sections (Figure 2). The ‘Documents’ tab gives access to general information: ‘Introduction’, ‘Class description’, ‘Publications’ and ‘Links’. Several useful tools are avail- able (‘Tools’) to classify and analyse peroxidases: ‘Search’ permits complex text queries on the database, ‘Blast’ allows a comparison between a query sequence and the peroxidases stored in PeroxiBase and, ‘FingerPrintscan’ and ‘PeroxiScan’ help classify a query sequence in the right group. The six following sections named ‘Classes’, ‘Organisms’, ‘Cellular localisations’, ‘Inducers’, ‘Repressors’ and ‘Tissue types’ permit the user to navigate within PeroxiBase using the speciﬁed criteria. Individual data sheets have been largely redesigned since the previous PeroxiBase publication (Figure 2). Last sequence changes, Reviewer and Last annotation changes ﬁelds exhibit the date of ﬁrst entry (or of last sequence modiﬁcation) with name of the contributor; the name of the curator who checked the entry, and the date of the last modiﬁcation in any sections with name of the contributor, respectively. In an attempt to set up a uniﬁed nomenclature (Name ﬁeld), we introduced a simple nomenclature based on spe- cies and class acronyms. The various original appellations have been conserved as synonyms in PeroxiBase. Class ﬁeld refers to the class the peroxidase belongs based on the new PeroxiScan tool. Cellular localisation, Tissue type, Figure 1. Schematic representation of the phylogenic relationships between the diﬀerent protein classes and families found in PeroxiBase.