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Nucleic Acids Res. 2014 Jan;42(Database issue):D654-9. doi: 10.1093/nar/gkt1048. Epub 2013 Nov 7.

DOOR 2.0: presenting operons and their functions through dynamic and integrated views.

Author information

1
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA, School of Mathematics, Shandong University, Jinan, Shandong 250100, China, College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China and College of Computer Science, Central China Normal University, Wuhan, Hubei 430079, China.

Abstract

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.

PMID:
24214966
PMCID:
PMC3965076
DOI:
10.1093/nar/gkt1048
[Indexed for MEDLINE]
Free PMC Article

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