ppdb: a plant promoter database
ppdb: a plant promoter database
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DOI：
10.1093/nar/gkm785
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发表时间：
2008-01-01
影响因子：
14.9
通讯作者：
Obokata, Junichi
中科院分区：
文献类型：
--
作者：
Yamamoto, Yoshiharu Y.;Obokata, Junichi
ppdb（www.ppdb.gene.nagoya-u.ac.jp）是提供拟南芥和水稻的启动子注释的植物启动子数据库。该数据库包含有关启动子结构、已从全长cDNA克隆中鉴定的转录起始位点（TSS）的信息，以及大量的TSS标签数据。在PPDB中，启动子结构由一组启动子元件决定，这些元件由称为短序列局部分布（LDSS）的位置敏感提取方法鉴定。通过使用该数据库，可以鉴定核心启动子结构、调节元件的存在和TSS簇的分布。虽然没有分化的启动子结构的植物物种之间的报道，有一些分歧的启动子元件的使用序列。因此，PPDB是基于启动子元件的物种特异性集合，而不是基于多个物种的通用基序。每个调控序列都超链接到文献信息、由植物顺式元件数据库提供的PLACE条目和含有调控序列的启动子列表。
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.