标题：DOOR 2.0: presenting operons and their functions through dynamic and integrated views
作者：Mao, Xizeng; Ma, Qin; Zhou, Chuan; Chen, Xin; Zhang, Hanyuan; Yang, Jincai; Mao, Fenglou; Lai, Wei; Xu, Ying
作者机构：[Mao, Xizeng; Ma, Qin; Zhou, Chuan; Chen, Xin; Zhang, Hanyuan; Mao, Fenglou; Lai, Wei; Xu, Ying] Univ Georgia, Dept Biochem & Mol Biol, Computat Syst 更多
通讯作者地址：[Xu, Y]Univ Georgia, Dept Biochem & Mol Biol, Computat Syst Biol Lab, Athens, GA 30602 USA.
来源：NUCLEIC ACIDS RESEARCH
摘要：We have recently developed a new version of the DOOR operon database, DOOR 2.0, which is available online at http://csbl.bmb.uga.edu/DOOR/ and will be updated on a regular basis. DOOR 2.0 contains genome-scale operons for 2072 prokaryotes with complete genomes, three times the number of genomes covered in the previous version published in 2009. DOOR 2.0 has a number of new features, compared with its previous version, including (i) more than 250 000 transcription units, experimentally validated or computationally predicted based on RNA-seq data, providing a dynamic functional view of the underlying operons; (ii) an integrated operon-centric data resource that provides not only operons for each covered genome but also their functional and regulatory information such as their cis-regulatory binding sites for transcription initiation and termination, gene expression levels estimated based on RNA-seq data and conservation information across multiple genomes; (iii) a high-performance web service for online operon prediction on user-provided genomic sequences; (iv) an intuitive genome browser to support visualization of user-selected data; and (v) a keyword-based Google-like search engine for finding the needed information intuitively and rapidly in this database.