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Nucleic Acids Research Advance Access published online on November 5, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn864
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Bionemo: molecular information on biodegradation metabolism

Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia and Ildefonso Cases*

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, E-28029, Madrid, Spain

*To whom correspondence should be addressed. Tel: +(34) 917 328 000; Fax: +(34) 912 246 980; Email: icases{at}cnio.es

Received October 1, 2008. Revised October 16, 2008. Accepted October 16, 2008.

Bionemo (http://bionemo.bioinfo.cnio.es) stores manually curated information about proteins and genes directly implicated in the Biodegradation metabolism. When possible, the database includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes. Thus, Bionemo is a unique resource that complements other biodegradation databases such as the University of Minessota Biocatalysis/Biodegradation Database, or Metarouter, which focus more on the biochemical aspects of biodegradation than in the nature of the biomolecules carrying out the reactions. Bionemo has been built by manually associating sequences database entries to biodegradation reactions, using the information extracted from published articles. Information on transcription units and their regulation was also extracted from the literature for biodegradation genes, and linked to the underlying biochemical network. In its current version, Bionemo contains sequence information for 324 reactions and transcription regulation information for more than 100 promoters and 100 transcription factors. The information in the Bionemo database is available via a web server and the full database is also downloadable as a PostgresSQL dump. To facilitate the programmatic use of the information contained in the database, an object-oriented Perl API is also provided.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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