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SubtiList


NAR Molecular Biology Database Collection entry number 96
Moszer, I.1, Jones, L.M.2, Moreira, S.1, Fabry, C.1, Danchin, A.3
1UnitÉ de GÉnÉtique des GÉnomes BactÉriens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
2Logiciels et Banques de DonnÉes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
3Hong Kong University-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China

Database Description

SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B. subtilis genome project (1), SubtiList provides a curated dataset of DNA and protein sequences, combined with the relevant annotations and functional assignments (2). Information about gene functions and products is continuously updated by linking relevant bibliographic references. Recently, sequence corrections arising from both systematic verifications and submissions by individual scientists were included in the reference genome sequence (3). SubtiList is based on a generic relational data schema and World-Wide Web interface developed for the handling of bacterial genomes, called GenoList. The WWW interface was designed to allow users to easily browse through genome data and retrieve information according to common biological queries. SubtiList also provides more elaborate tools, such as pattern searching, which are tightly connected to the overall browsing system. SubtiList is accessible at the URL http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at the URL http://genolist.pasteur.fr/.

Acknowledgements

Initial development stages (4) were performed in the framework of the European B. subtilis genome project (European Commission Biotechnology program — contracts BIO2-CT93-0272, BIO2-CT94-2011, BIO4-CT96-0655), coordinated by F. Kunst and supported by the BACillus Industrial Platform (BACIP). We thank the contribution at various stages of P. Glaser, A. HÉnaut, C. MÉdigue, M. Pupin, and A. Viari. We acknowledge the fruitful collaboration with A. Bairoch and the SWISS-PROT team.

References

1. Kunst,F., Ogasawara,N., Moszer,I., Albertini,A.M., Alloni,G., Azevedo,V., Bertero,M.G., BessiÈres,P., Bolotin,A., Borchert,S., et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature, 390,
249-256.
2. Moszer,I. (1998) The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis. FEBS Lett.,
430, 28-36.
3. MÉdigue,C., Rose,M., Viari,A. and Danchin,A. (1999) Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence. Genome Res., 9, 1116-1127.
4. Moszer,I., Glaser,P. and Danchin,A. (1995) SubtiList: a relational database for the Bacillus subtilis genome. Microbiology, 141,
261-268.


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