Abstract
ppdb (http://ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information about promoter structures, and also transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. Promoter structures are recognized by sets of promoter elements identified by a position-sensitive extraction method called LDSS. Using the database, the core promoter structure, the presence of regulatory elements, and the distribution of TSS clusters are identified. One of the unique features of ppdb is utilization of species-specific sets of promoter elements, rather than application of general motifs for multiple species. Since establishment in June, 2007, more than 100,000 accesses from 39 countries have been achieved for the rest of the year.
