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SubtiList

http://genolist.pasteur.fr/SubtiList/

Moszer, I.¹, Jones, L.M.², Moreira, S.¹, Fabry, C.¹, Danchin, A.³

¹UnitÈ de GÈnÈtique des GÈnomes BactÈriens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
²Logiciels et Banques de DonnÈes, 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

Contact   moszer@pasteur.fr

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/.

Recent Developments

See abstract.

Acknowledgements

Initial development stages (4) were performed in the framework of the European B. subtilis genome project (European Commission Biotechnology program ó 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. HÈnaut, C. MÈdigue, 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., BessiËres,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. MÈdigue,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.

Category   Genomic Databases

Go to the abstract in the NAR 2002 Database Issue.