PeroxiBase
Encyclopedia
The PeroxiBase database has been created at the University of Geneva
University of Geneva
The University of Geneva is a public research university located in Geneva, Switzerland.It was founded in 1559 by John Calvin, as a theological seminary and law school. It remained focused on theology until the 17th century, when it became a center for Enlightenment scholarship. In 1873, it...

 (Switzerland
Switzerland
Switzerland name of one of the Swiss cantons. ; ; ; or ), in its full name the Swiss Confederation , is a federal republic consisting of 26 cantons, with Bern as the seat of the federal authorities. The country is situated in Western Europe,Or Central Europe depending on the definition....

) at the end of 2003, by two plant biologists specialised in the study of plant peroxidase
Peroxidase
Peroxidases are a large family of enzymes that typically catalyze a reaction of the form:For many of these enzymes the optimal substrate is hydrogen peroxide, but others are more active with organic hydroperoxides such as lipid peroxides...

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
Peroxidase
Peroxidases are a large family of enzymes that typically catalyze a reaction of the form:For many of these enzymes the optimal substrate is hydrogen peroxide, but others are more active with organic hydroperoxides such as lipid peroxides...

 sequences can now be found in the PeroxiBase.

The database is hosted by the Swiss Institute of Bioinformatics
Swiss Institute of Bioinformatics
The Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland...

.

Peroxidase sequences come from other general public databases (NCBI
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...

, TIGR
The Institute for Genomic Research
The Institute for Genomic Research was a non-profit genomics research institute founded in 1992 by Craig Venter in Rockville, Maryland, United States. It is now a part of the J. Craig Venter Institute.-History:...

, UniProt KnowledgeBase
UniProt
UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...

: 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
The source of this article is wikipedia, the free encyclopedia.  The text of this article is licensed under the GFDL.
 
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