The PeroxiBase database has been created at the
University of Geneva
The University of Geneva (French: ''Université de Genève'') is a public research university located in Geneva, Switzerland. It was founded in 1559 by John Calvin as a theological seminary. It remained focused on theology until the 17th centu ...
(
Switzerland
). Swiss law does not designate a ''capital'' as such, but the federal parliament and government are installed in Bern, while other federal institutions, such as the federal courts, are in other cities (Bellinzona, Lausanne, Luzern, Neuchâtel ...
) at the end of 2003, by two plant biologists specialised in the study of plant
peroxidase
Peroxidases or peroxide reductases ( EC numberbr>1.11.1.x are a large group of enzymes which play a role in various biological processes. They are named after the fact that they commonly break up peroxides.
Functionality
Peroxidases typically ca ...
s. It was first limited to class III peroxidases (plant peroxidases) and was then expanded to include all possible haem and non-haem peroxidase protein sequences. Many researchers and bioinformaticians from the University of Geneva joined their efforts to develop the database and rapidly increase the number of peroxidase sequences. Since 2005, the database accepts external contributions, which are verified by PeroxiBase curators. The majority of haem and non-haem
peroxidase
Peroxidases or peroxide reductases ( EC numberbr>1.11.1.x are a large group of enzymes which play a role in various biological processes. They are named after the fact that they commonly break up peroxides.
Functionality
Peroxidases typically ca ...
sequences can now be found in the PeroxiBase.
The database is hosted by the
Swiss Institute of Bioinformatics
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
The institute was established on 30 March 1998 and its mission is to provide core bioinfor ...
.
Peroxidase sequences come from other general public databases (
NCBI
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...
,
TIGR
TIGR, an abbreviation for ''Trst'', ''Istra'', ''Gorica'', and ''Reka'', full name Revolutionary Organization of the Julian March T.I.G.R. ( sl, Revolucionarna organizacija Julijske krajine T.I.G.R.), was a militant anti-fascist and insurgent or ...
,
UniProt KnowledgeBase: all the databases used are listed in the PeroxiBase), either as pre-existing annotated sequences, or from raw data (whole genomic sequencing projects).
Goals of the PeroxiBase
* To publicly (non-profit) provide the scientific community with a centralised platform regrouping information on peroxidase sequences. Possible applications: faster sequence search, phylogenetic analysis, expression profile determination
* To manually re-annotate existing sequences (automated annotation sometimes leads to wrong predictions)
* To acquire new sequences that are not yet available in other databases: non-annotated genomes, external contributions from sequencing groups
References
External links
Database homepage
{{Peroxidases
Biological databases
University of Geneva