DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Mao, Xizeng 1,2; Ma, Qin 1,2; Zhou, Chuan 1,3; Chen, Xin 1,4; Zhang, Hanyuan 1,4; Yang, Jincai 5; Mao, Fenglou 1; Lai, Wei 1; Xu, Ying 1,2,4,*
[Miscellaneous Article] Nucleic Acids Research. 42(D1):D654-D659, January 1, 2014.

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: 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.

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