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Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis

Lookup NU author(s): Dr Ulrike Mader, Dr Leendert Hamoen

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Abstract

Bacillus subtilis is the model organism for a large group of Gram-positive bacteria, the Firmicutes. Several online databases have been established over time to manage its genetic and metabolic information, but they differ greatly in their rate of update and their focus on B. subtilis. Therefore, a European systems biology consortium called for an integrated solution that empowers its users to enrich online content. To meet this goal we created SubtiWiki and SubtiPathways, two complementary online tools for gene and pathway information on B. subtilis 168. SubtiWiki (http://subtiwiki.uni-goettingen.de/) is a scientific wiki for all genes of B. subtilis and their protein or RNA products. Each gene page contains a summary of the most important information; sections on the gene, its product and expression; sections concerning biological materials and laboratories; and a list of references. SubtiWiki has been seeded with key content and can be extended by any researcher after a simple registration, thus keeping it always up to date. As a complement, SubtiPathways (http://subtipathways.uni-goettingen.de/) is an online tool for navigation of the metabolism of B. subtilis and its regulation. Each SubtiPathways diagram presents a metabolic pathway with its participating enzymes, together with the regulatory mechanisms that act on their expression and activity, in an intuitive interface that is based on Google Maps. Together, SubtiWiki and SubtiPathways provide an integrated view of the processes that make up B. subtilis and its components, making it the most comprehensive web resource for B. subtilis researchers.


Publication metadata

Author(s): Lammers CR, Florez LA, Schmeisky AG, Roppel SF, Mader U, Hamoen L, Stulke J

Publication type: Article

Publication status: Published

Journal: Microbiology

Year: 2010

Volume: 156

Pages: 849-859

Print publication date: 01/03/2010

ISSN (print): 1350-0872

ISSN (electronic): 1465-2080

Publisher: Society for General Microbiology

URL: http://dx.doi.org/10.1099/mic.0.035790-0

DOI: 10.1099/mic.0.035790-0


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Funding

Funder referenceFunder name
Fonds der Chemischen Industrie
Studienforderwerk Klaus Murmann der Stiftung der Deutschen Wirtschaft
University of Gottingen
PtJ-BIO/0313978DFederal Ministry of Education

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