The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

被引:701
作者
Davis, James J. [1 ,2 ,6 ]
Wattam, Alice R. [2 ,3 ]
Aziz, Ramy K. [4 ,5 ]
Brettin, Thomas [1 ,6 ]
Butler, Ralph [2 ,7 ]
Butler, Rory M. [2 ]
Chlenski, Philippe [8 ]
Conrad, Neal [1 ,2 ]
Dickerman, Allan [3 ]
Dietrich, Emily M. [1 ,6 ]
Gabbard, Joseph L. [9 ]
Gerdes, Svetlana [8 ]
Guard, Andrew [1 ]
Kenyon, Ronald W. [3 ]
Machi, Dustin [3 ]
Mao, Chunhong [3 ]
Murphy-Olson, Dan [1 ,6 ]
Nguyen, Marcus [1 ,2 ]
Nordberg, Eric K. [10 ]
Olsen, Gary J. [11 ,12 ]
Olson, Robert D. [1 ,2 ]
Overbeek, Jamie C. [1 ,2 ]
Overbeek, Ross [1 ]
Parrello, Bruce [1 ,2 ]
Pusch, Gordon D. [8 ]
Shukla, Maulik [1 ,2 ]
Thomas, Chris [1 ]
VanOeffelen, Margo [8 ]
Vonstein, Veronika [8 ]
Warren, Andrew S. [3 ]
Xia, Fangfang [1 ,2 ]
Xie, Dawen [3 ]
Yoo, Hyunseung [1 ,2 ]
Stevens, Rick [6 ,13 ]
机构
[1] Univ Chicago, Univ Chicago Consortium Adv Sci & Engn, Chicago, IL 60637 USA
[2] Argonne Natl Lab, Div Data Sci & Learning, Argonne, IL 60439 USA
[3] Univ Virginia, Biocomplex Inst & Initiat, Charlottesville, VA 22904 USA
[4] Cairo Univ, Fac Pharm, Dept Microbiol & Immunol, Cairo 11562, Egypt
[5] Cairo Univ, Ctr Genome & Microbiome Res, Cairo 11562, Egypt
[6] Argonne Natl Lab, Comp Environm & Life Sci, 9700 S Cass Ave, Argonne, IL 60439 USA
[7] Middle Tennessee State Univ, Murfreesboro, TN 37132 USA
[8] Fellowship Interpretat Genomes, Burr Ridge, IL 60527 USA
[9] Virginia Tech, Blacksburg, VA 24061 USA
[10] Virginia Tech Univ, Transportat Inst, Blacksburg, VA 24061 USA
[11] Univ Illinois, Dept Microbiol, 131 Burrill Hall, Urbana, IL 61801 USA
[12] Univ Illinois, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA
[13] Univ Chicago, Dept Comp Sci, Chicago, IL 60637 USA
关键词
SEQUENCE; ALGORITHM; ALIGNMENT;
D O I
10.1093/nar/gkz943
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.
引用
收藏
页码:D606 / D612
页数:7
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