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

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成果类型:
期刊论文
作者:
Mao, Xizeng;Ma, Qin;Zhou, Chuan;Chen, Xin;Zhang, Hanyuan;Yang, Jincai(杨进才);Mao, Fenglou;Lai, Wei;Xu, Ying*
通讯作者:
Xu, Ying
作者机构:
[Chen, Xin; Zhang, Hanyuan; Zhou, Chuan; Mao, Fenglou; Xu, Ying; Mao, Xizeng; Lai, Wei; Ma, Qin] Univ Georgia, Dept Biochem & Mol Biol, Computat Syst Biol Lab, Athens, GA 30602 USA.
[Chen, Xin; Zhang, Hanyuan; Zhou, Chuan; Mao, Fenglou; Xu, Ying; Mao, Xizeng; Lai, Wei; Ma, Qin] Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA.
[Xu, Ying; Mao, Xizeng; Ma, Qin] Oak Ridge Natl Lab, BioEnergy Sci Ctr BESC, Oak Ridge, TN 37831 USA.
[Zhou, Chuan] Shandong Univ, Sch Math, Jinan 250100, Shandong, Peoples R China.
[Chen, Xin; Zhang, Hanyuan; Xu, Ying] Jilin Univ, Coll Comp Sci & Technol, Changchun 130012, Jilin, Peoples R China.
通讯机构:
[Xu, Ying] U
Univ Georgia, Dept Biochem & Mol Biol, Computat Syst Biol Lab, Athens, GA 30602 USA.
语种:
英文
期刊:
Nucleic Acids Research
ISSN:
0305-1048
年:
2014
卷:
42
期:
D1
页码:
D654-D659
基金类别:
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
机构署名:
本校为其他机构
院系归属:
生命科学学院
数学与统计学学院
计算机学院
摘要:
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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