DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants.
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants.
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DOI：
10.1093/nar/gki097
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发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Patthy L
中科院分区：
文献类型：
--
作者：
Barta E;Sebestyén E;Pálfy TB;Tóth G;Ortutay CP;Patthy L
DOOP(http://doop.abc.hu/))是一个真核生物启动子序列(上游区域)的数据库，旨在促进物种间保守的调控位点的识别。使用人类和拟南芥基因的第一外显子作为BLAST搜索的查询，以从脊索植物和病毒科物种中收集最接近的同源第一外显子序列。这些第一外显子上游多达3000个碱基的DNA片段构成了同源启动子数据库中脊索和植物部分的簇。DOOP第1.0版包含来自284个不同物种的21个 061脊索簇和来自269个不同物种的7,548个植物簇。该数据库可用于从不同物种中寻找和检索给定基因的启动子序列，也适用于在同源上游区域中寻找最琐碎的保守序列块。用户可以使用序列或文本(注释)搜索doop，以找到各种基因的启动子簇。除了序列数据外，还可以用图形方式查看来自多个比对的保守序列块的位置、重复元件的位置以及真核生物启动子数据库(EPD)中已知的转录起始点的位置。
DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically.