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. 2013 Jan;41(Database issue):D441-4.
doi: 10.1093/nar/gks1083. Epub 2012 Nov 24.

PeroxiBase: a database for large-scale evolutionary analysis of peroxidases

Nizar Fawal  1 , Qiang Li, Bruno Savelli, Marie Brette, Gisele Passaia, Maxime Fabre, Catherine Mathé, Christophe Dunand
Affiliations

PeroxiBase: a database for large-scale evolutionary analysis of peroxidases

Nizar Fawal et al. Nucleic Acids Res. 2013 Jan.

Abstract

The PeroxiBase (http://peroxibase.toulouse.inra.fr/) is a specialized database devoted to peroxidases' families, which are major actors of stress responses. In addition to the increasing number of sequences and the complete modification of the Web interface, new analysis tools and functionalities have been developed since the previous publication in the NAR database issue. Nucleotide sequences and graphical representation of the gene structure can now be included for entries containing genomic cross-references. An expert semi-automatic annotation strategy is being developed to generate new entries from genomic sequences and from EST libraries. Plus, new internal and automatic controls have been included to improve the quality of the entries. To compare gene structure organization among families' members, two new tools are available, CIWOG to detect common introns and GECA to visualize gene structure overlaid with sequence conservation. The multicriteria search tool was greatly improved to allow simple and combined queries. After such requests or a BLAST search, different analysis processes are suggested, such as multiple alignments with ClustalW or MAFFT, a platform for phylogenetic analysis and GECA's display in association with a phylogenetic tree. Finally, we updated our family specific profiles implemented in the PeroxiScan tool and made new profiles to consider new sub-families.

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Figures

Figure 1.
Figure 1.
Numbers of organisms in the PeroxiBase in the five major kingdoms (A) and numbers of entries in the PeroxiBase in every kingdom (B).
Figure 2.
Figure 2.
Schematic representation of the workflow for collection, annotation and analysis of sequences. Each step of the individual curration and tools available for the analysis are described elsewhere.
See this image and copyright information in PMC

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