期刊
NUCLEIC ACIDS RESEARCH
卷 42, 期 D1, 页码 D654-D659出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt1048
关键词
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资金
- National Science Foundation [DEB-0830024]
- DOE BioEnergy Science Center [DE-PS02-717 06ER64304, DOE 4000063512]
- Office of Biological and Environmental Research in the Department of Energy Office of Science
- Direct For Biological Sciences [0830024] Funding Source: National Science Foundation
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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