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DBTBS


NAR Molecular Biology Database Collection entry number 31
Makita Y.1, De Hoon M.J.L.2 and Nakai, K.3
1Pasteur Institute, Unit of Genetics of Bacterial Genomes, Paris, France
2Columbia University, Center for Computational Biology and Bioinformatics, New York, NY, USA
3Human Genome Center, Insisitute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan

Database Description

With the entire genome sequence of Bacillus subtilis now determined, one of the next major targets of B. subtilis genomics is to elucidate its complete gene regulatory network. To this end, the results of systematic experiments should be compared with the rich source of individual experimental results accumulated so far. We therefore constructed the DBTBS database, containing a collection of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of B. subtilis genes. Its current version is constructed by surveying 873 references and contains the information of 116 binding factors and 1253 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. Multiple alignments of upstream sequences between B. halodurans, B. stearothermophilus, and B. subtilis are also shown.

Recent Developments

The DBTBS database was recently reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. DBTBS now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)).

Acknowledgements

We are grateful to Naotake Ogasawara for useful comments, and Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Mitsuteru Nakao and Yasutaro Fujita, who have contributed to earlier versions of this database. This work was partly supported by a Grant-in Aid for Scientific Research on Priority Areas 'Genome Information Science' from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

References

1. Ishii, T. et al. (2001). Nucleic Acids Res. 29, 278-280.
2. Makita, Y. et al. (2004). Nucleic Acids Res. 32, D75-D77


Go to the abstract in the NAR 2004 Database Issue.
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