DOOR


28968679	DOOR: a prokaryotic operon database for genome analyses and functional inference. [PMID: 28968679] Cao H, Ma Q, Chen X, Xu Y. Abstract The rapid accumulation of fully sequenced prokaryotic genomes provides unprecedented information for biological studies of bacterial and archaeal organisms in a systematic manner. Operons are the basic functional units for conducting such studies. Here, we review an operon database DOOR (the Database of prOkaryotic OpeRons) that we have previously developed and continue to update. Currently, the database contains 6?975?454 computationally predicted operons in 2072 complete genomes. In addition, the database also contains the following information: (i) transcriptional units for 24 genomes derived using publicly available transcriptomic data; (ii) orthologous gene mapping across genomes; (iii) 6408 cis-regulatory motifs for transcriptional factors of some operons for 203 genomes; (iv) 3?456?718 Rho-independent terminators for 2072 genomes; as well as (v) a suite of tools in support of applications of the predicted operons. In this review, we will explain how such data are computationally derived and demonstrate how they can be used to derive a wide range of higher-level information needed for systems biology studies to tackle complex and fundamental biology questions. Brief Bioinform. 2019:20(4) \| 14 Citations (from Europe PMC, 2025-03-22)
24214966	DOOR 2.0: presenting operons and their functions through dynamic and integrated views. [PMID: 24214966] Mao X, Ma Q, Zhou C, Chen X, Zhang H, Yang J, Mao F, Lai W, Xu Y. 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. Nucleic Acids Res. 2014:42(Database issue) \| 117 Citations (from Europe PMC, 2025-03-22)
18988623	DOOR: a database for prokaryotic operons. [PMID: 18988623] Mao F, Dam P, Chou J, Olman V, Xu Y. Abstract We present a database DOOR (Database for prOkaryotic OpeRons) containing computationally predicted operons of all the sequenced prokaryotic genomes. All the operons in DOOR are predicted using our own prediction program, which was ranked to be the best among 14 operon prediction programs by a recent independent review. Currently, the DOOR database contains operons for 675 prokaryotic genomes, and supports a number of search capabilities to facilitate easy access and utilization of the information stored in it. (1) Querying the database: the database provides a search capability for a user to find desired operons and associated information through multiple querying methods. (2) Searching for similar operons: the database provides a search capability for a user to find operons that have similar composition and structure to a query operon. (3) Prediction of cis-regulatory motifs: the database provides a capability for motif identification in the promoter regions of a user-specified group of possibly coregulated operons, using motif-finding tools. (4) Operons for RNA genes: the database includes operons for RNA genes. (5) OperonWiki: the database provides a wiki page (OperonWiki) to facilitate interactions between users and the developer of the database. We believe that DOOR provides a useful resource to many biologists working on bacteria and archaea, which can be accessed at http://csbl1.bmb.uga.edu/OperonDB. Nucleic Acids Res. 2009:37(Database issue) \| 256 Citations (from Europe PMC, 2025-03-22)

DOOR: a prokaryotic operon database for genome analyses and functional inference. [PMID: 28968679]

Cao H, Ma Q, Chen X, Xu Y.

The rapid accumulation of fully sequenced prokaryotic genomes provides unprecedented information for biological studies of bacterial and archaeal organisms in a systematic manner. Operons are the basic functional units for conducting such studies. Here, we review an operon database DOOR (the Database of prOkaryotic OpeRons) that we have previously developed and continue to update. Currently, the database contains 6?975?454 computationally predicted operons in 2072 complete genomes. In addition, the database also contains the following information: (i) transcriptional units for 24 genomes derived using publicly available transcriptomic data; (ii) orthologous gene mapping across genomes; (iii) 6408 cis-regulatory motifs for transcriptional factors of some operons for 203 genomes; (iv) 3?456?718 Rho-independent terminators for 2072 genomes; as well as (v) a suite of tools in support of applications of the predicted operons. In this review, we will explain how such data are computationally derived and demonstrate how they can be used to derive a wide range of higher-level information needed for systems biology studies to tackle complex and fundamental biology questions.

Brief Bioinform. 2019:20(4) | 14 Citations (from Europe PMC, 2025-03-22)

DOOR 2.0: presenting operons and their functions through dynamic and integrated views. [PMID: 24214966]

Mao X, Ma Q, Zhou C, Chen X, Zhang H, Yang J, Mao F, Lai W, Xu Y.

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.

Nucleic Acids Res. 2014:42(Database issue) | 117 Citations (from Europe PMC, 2025-03-22)

DOOR: a database for prokaryotic operons. [PMID: 18988623]

Mao F, Dam P, Chou J, Olman V, Xu Y.

Abstract

We present a database DOOR (Database for prOkaryotic OpeRons) containing computationally predicted operons of all the sequenced prokaryotic genomes. All the operons in DOOR are predicted using our own prediction program, which was ranked to be the best among 14 operon prediction programs by a recent independent review. Currently, the DOOR database contains operons for 675 prokaryotic genomes, and supports a number of search capabilities to facilitate easy access and utilization of the information stored in it. (1) Querying the database: the database provides a search capability for a user to find desired operons and associated information through multiple querying methods. (2) Searching for similar operons: the database provides a search capability for a user to find operons that have similar composition and structure to a query operon. (3) Prediction of cis-regulatory motifs: the database provides a capability for motif identification in the promoter regions of a user-specified group of possibly coregulated operons, using motif-finding tools. (4) Operons for RNA genes: the database includes operons for RNA genes. (5) OperonWiki: the database provides a wiki page (OperonWiki) to facilitate interactions between users and the developer of the database. We believe that DOOR provides a useful resource to many biologists working on bacteria and archaea, which can be accessed at http://csbl1.bmb.uga.edu/OperonDB.

Nucleic Acids Res. 2009:37(Database issue) | 256 Citations (from Europe PMC, 2025-03-22)

URL:	http://csbl.bmb.uga.edu/DOOR/
Full name:	Database of Prokaryotic Operons
Description:	DOOR, which contains computationally predicted operons of >2,000 sequenced prokaryotic genomes, is a useful resource to many biologists working on bacteria and archaea.
Year founded:	2009
Last update:	2014
Version:	v2.0
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA RNA
Data object:	Archaea Bacteria
Database category:	Gene genome and annotation
Major species:	NA
Keywords:	computationally predicted operon prokaryotic genome motif sequences

University/Institution:	University of Georgia
Address:	Computational Systems Biology Laboratory,Department of Biochemistry and Molecular Biology,and Institute of Bioinformatics,University of Georgia,Athens,GA 30602,USA
City:	Athens
Province/State:	GA
Country/Region:	United States
Contact name (PI/Team):	Ying Xu
Contact email (PI/Helpdesk):	xyn@uga.edu

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Database Commons a catalog of worldwide biological databases