期刊论文

Xu, Ying

英文

Nucleic Acids Research

0305-1048

2014

42

D1

D654-D659

10.1093/nar/gkt1048

National Science FoundationNational Science Foundation (NSF) [DEB-0830024]; DOE BioEnergy Science CenterUnited States Department of Energy (DOE) [DE-PS02-717 06ER64304, DOE 4000063512]; Office of Biological and Environmental Research in the Department of Energy Office of Science; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [0830024] Funding Source: National Science Foundation

本校为其他机构

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.