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Nucleic Acids Research Advance Access originally published online on October 25, 2007
Nucleic Acids Research 2008 36(Database issue):D93-D96; doi:10.1093/nar/gkm910
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Nucleic Acids Research, 2008, Vol. 36, Database issue D93-D96
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-com

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

Nicolas Sierro1, Yuko Makita2, Michiel de Hoon2 and Kenta Nakai1,*

1Human Genome Center, The Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 and 2Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan

* To whom correspondence should be addressed. Tel: +81 3 5449 5131; Fax: +81 3 5449 5133; Email: knakai{at}ims.u-tokyo.ac.jp

Received September 15, 2007. Revised October 5, 2007. Accepted October 5, 2007.

DBTBS, first released in 1999, is a reference database on transcriptional regulation in Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition sequences and the genes they regulate. Since the previous release, the original content was extended by the addition of the data contained in 569 new publications, the total of which now reaches 947. The number of B. subtilis promoters annotated in the database was more than doubled to 1475. In addition, 463 experimentally validated B. subtilis operons and their terminators have been included. Given the increase in the number of fully sequenced bacterial genomes, we decided to extend the usability of DBTBS in comparative regulatory genomics. We therefore created a new section on the conservation of the upstream regulatory sequences between homologous genes in 40 Gram-positive bacterial species, as well as on the presence of overrepresented hexameric motifs that may have regulatory functions. DBTBS can be accessed at: http://dbtbs.hgc.jp.


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