ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes
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DOI：
10.1093/bioinformatics/btl546
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发表时间：
2007-01-01
期刊：
影响因子：
5.8
通讯作者：
Ovcharenko, Ivan
中科院分区：
文献类型：
--
作者：
Loots, Gabriela;Ovcharenko, Ivan
动机：DNA序列的进化保守性为基因组中功能元件的鉴定提供了一种工具。我们已经创建了一个数据库的进化保守区（ECR）的脊椎动物基因组，名为ECR基地，这是从一个收集的全基因组比对ECR浏览器。ECRbase的特点是一个数据库的同线块，概括了进化的重排在脊椎动物和一个全面的收集启动子在所有脊椎动物基因组中产生的基因注释的多个来源。该数据库还包含一个集合的注释转录因子结合位点（TFBS）在进化保守和启动子元件。ECRbase目前包括人类、恒河猴、狗、负鼠、大鼠、小鼠、鸡、青蛙、斑马鱼和河豚的基因组。它可以在http://ecrbase.dcode.org上免费获得。
Motivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at http://ecrbase.dcode.org.