Inducer and Repressor ﬁelds present data concerning the gene and protein expressions. These ﬁelds use ﬁxed terms. Best BLASTp hits ﬁeld reports the ﬁve closest hits to this entry obtained from daily updated BLAST searches. Protein ref, DNA ref, mRNA ref and Cluster/prediction ref ﬁelds refer to hyperlinks protein, DNA, mRNA sequences and cluster respectively. PeroxiBase entries are cross-referenced in UniProtKB (SwissProt/TREMBL). The data are stored in a MySQL relational database and the web interface is made of PHP and CGI/Perl scripts. DATA ACQUISITION AND INTEGRATION The automatic annotation of the complete genomes of numerous organisms and the automatic clustering and assembling of EST sequences led to the identiﬁcation of numerous sequences coding for diﬀerent peroxidase families and superfamilies. However, the automatic pro- cessing of the sequences is known to be of poor quality or not as speciﬁc as expected. Using the highly conserved motifs of each peroxidase class, manual annotation and editing can clearly identify the correct sequences even in low-quality sequences. In order to increase data reliability, Nucleic Acids Research, 2009, Vol. 37, Database issue D263 each new entry is individually controlled by a database curator. Each cross-reference is veriﬁed by the reviewer. The quality of the sequence is also examined by perform- ing a sequence alignment with the other homologous sequences. Thank to the continuous release of numerous genome sequencing projects (525 in March 2007 and 843 in August 2008 according to the Genomes OnLine Database (11)) and EST libraries, existing entries can be updated and, as more annotated sequences are integrated, the organism coverage is also increased. Existing entries are frequently veriﬁed and updated if any changes have occurred. NEW CLASSIFICATION TOOLS FOR PEROXIDASES To facilitate the classiﬁcation of newly sequenced peroxi- dase proteins, we have developed a tool, based on PROSITE proﬁle methodology that takes advantage of the manually curated hierarchical classiﬁcation of PeroxiBase. One major problem with subfamily classiﬁca- tion is the diﬃculty in separating proteins due to their high degree of similarity at the sequence level. The main princi- ple of our new approach is to build a PROSITE proﬁle on Figure 2. Screenshot of one entry and description of the toolbar. The toolbar includes various sections. ‘Documents’ contains ‘Introduction’, ‘Class description’, ‘Publications’ (related to PeroxiBase) and ‘Links’ (speciﬁc and general databases). ‘Tools’ menu contains the following sections: ‘Search’ (multi criteria), ‘Blast’, ‘PeroxiScan’ and ‘FingerPrintscan’.