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Nucleic Acids Research Advance Access originally published online on October 18, 2007
Nucleic Acids Research 2008 36(Database issue):D977-D981; doi:10.1093/nar/gkm785
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Nucleic Acids Research, 2008, Vol. 36, Database issue D977-D981
© 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-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Articles

ppdb: a plant promoter database

Yoshiharu Y. Yamamoto and Junichi Obokata*

Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan

*To whom correspondence should be addressed. Tel/Fax: +81-52-789-3083; Email: obokata{at}gene.nagoya-u.ac.jp

Received August 14, 2007. Revised September 13, 2007. Accepted September 17, 2007.

ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are determined by sets of promoter elements identified by a position-sensitive extraction method called local distribution of short sequences (LDSS). By using this database, the core promoter structure, the presence of regulatory elements and the distribution of TSS clusters can be identified. Although no differentiation of promoter architecture among plant species has been reported, there is some divergence of utilized sequences for promoter elements. Therefore, ppdb is based on species-specific sets of promoter elements, rather than on general motifs for multiple species. Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence.


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