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LeptoList


NAR Molecular Biology Database Collection entry number 521
Cédric Cabau1, Virginie Cubas1, Gang Fang1,3, Christine Ho1, Zhou Yu1, Ivan Moszer2,3, Antoine Danchin1,3
1HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
2Plateforme Integration et Analyse des Génomes, Génopole, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
3Unité de Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France

Database Description

LeptoList is the reference database dedicated to the genome of Leptospira interrogans serovar Lai, the paradigm of leptospirosis causative agents (1). It has been developed as a spin-off of the B. subtilis genome project (2), GenoList provides a data schema for the management of DNA and protein sequences, combined with the relevant annotations and functional assignments (3). Information about gene functions and products is updated by a curating team. LeptoList is based on a generic relational data schema and World-Wide Web interface developed for the handling of bacterial genomes, GenoList. The underlying DataBase Management System used in the Hong Kong based databases is MySQL. The WWW interface was designed to allow users to easily browse through genome data and retrieve information according to common biological queries. LeptoList also provides more elaborate tools, such as pattern searching, which are tightly connected to the overall browsing system. LeptoList is accessible at the URL http://www.bioinfo.hku.hk/LeptoList/. Similar bacterial databases (for Bacillus anthracis, Bacillus cereus, Neisseria meningitidis, Pseudomonas aeruginosa, Staphylococcus epidermidis, Streptomyces coelicolor, Thermoanaerobacter tencongensis, Vibrio cholerae, Xylella fastidiosa, etc.) are accessible at the URL http://www.hkupasteur.hku.hk/hkuip/databases.html

Acknowledgements

This effort is sponsored by the Innovation and Technology Fund (http://www.info.gov.hk/itc/) of the government of the SAR Hong Kong, China (programme BIOSUPPORT, http://www.bioinfo.hku.hk/), granted to A. Danchin for the creation of the HKU-Pasteur Research Centre. Initial development stages (4) of GenoList 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 F. Cheung, 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. Ren S.X. , Fu G., Jiang X.G.,. Zeng R, Miao Y.G., Xu H., Zhang Y.X., Xiong H., Lu G., Lu L.F., Jiang H.Q., Jia J., Tu Y.F., Jiang J.X., Gu W.Y., Zhang Y.Q., Cai Z., ShengH.H. , Yin H.F., Zhang Y., Zhu G.F., Wan M., Huang H.L., Qian Z., Wang S.Y., Ma W., Yao Z.J., Shen Y., Qiang B.Q., Xia Q.C., Guo X.K., Danchin A., Saint Girons I., Somerville R.L., Wen Y.M., Shi M.H., Chen Z., Xu J.G. & Zhao G.P. Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature (2003) 422:888-893.
2. Kunst,F., Ogasawara, N., Moszer,I., Albertini,A.M., Alloni,G., Azevedo,V., Bertero, M.G., Bessières,P., Bolotin,A., Borchert,S., et al. and A. Danchin (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature, 390, 249-256.
3. Moszer,I. (1998) The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis. FEBS Lett., 430, 28-36.
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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