The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities-Reference-Cited by-同舟云学术

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

Published:2019-10-31 Issue: Volume: Page:
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Davis James J¹²,Wattam Alice R²³,Aziz Ramy K⁴⁵,Brettin Thomas¹⁶,Butler Ralph²⁷,Butler Rory M²,Chlenski Philippe⁸,Conrad Neal¹²,Dickerman Allan³,Dietrich Emily M¹⁶,Gabbard Joseph L⁹,Gerdes Svetlana⁸^ORCID,Guard Andrew¹,Kenyon Ronald W³,Machi Dustin³,Mao Chunhong³,Murphy-Olson Dan¹⁶,Nguyen Marcus¹²,Nordberg Eric K¹⁰,Olsen Gary J¹¹¹²,Olson Robert D¹²,Overbeek Jamie C¹²,Overbeek Ross¹,Parrello Bruce¹²,Pusch Gordon D⁸,Shukla Maulik¹²,Thomas Chris¹,VanOeffelen Margo⁸,Vonstein Veronika⁸,Warren Andrew S³,Xia Fangfang¹²,Xie Dawen³,Yoo Hyunseung¹²,Stevens Rick⁶¹³

Affiliation:

1. University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA

2. Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA

3. Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA

4. Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt

5. Center for Genome and Microbiome Research, Cairo University, 11562 Cairo, Egypt

6. Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA

7. Middle Tennessee State University, Murfreesboro, TN 37132, USA

8. Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA

9. Virginia Tech, Blacksburg, VA 24061, USA

10. Transportation Institute, Virginia Tech University, Blacksburg, VA 24061, USA

11. Department of Microbiology, University of Illinois, Urbana, IL 61801, USA

12. Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA

13. University of Chicago, Department of Computer Science, Chicago, IL 60637, USA

Abstract

Abstract 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.

Funder

National Institute of Allergy and Infectious Diseases

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

http://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkz943/30335558/gkz943.pdf

Reference53 articles.

1. PATRIC: the VBI pathosystems resource integration center;Snyder;Nucleic Acids Res.,2006

2. PATRIC, the bacterial bioinformatics database and analysis resource;Wattam;Nucleic Acids Res.,2013

3. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center;Wattam;Nucleic Acids Res.,2016