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. 2020 Jan 8;48(D1):D606-D612.
doi: 10.1093/nar/gkz943.

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

James J Davis  1   2 , Alice R Wattam  2   3 , Ramy K Aziz  4   5 , Thomas Brettin  1   6 , Ralph Butler  2   7 , Rory M Butler  2 , Philippe Chlenski  8 , Neal Conrad  1   2 , Allan Dickerman  3 , Emily M Dietrich  1   6 , Joseph L Gabbard  9 , Svetlana Gerdes  8 , Andrew Guard  1 , Ronald W Kenyon  3 , Dustin Machi  3 , Chunhong Mao  3 , Dan Murphy-Olson  1   6 , Marcus Nguyen  1   2 , Eric K Nordberg  10 , Gary J Olsen  11   12 , Robert D Olson  1   2 , Jamie C Overbeek  1   2 , Ross Overbeek  1 , Bruce Parrello  1   2 , Gordon D Pusch  8 , Maulik Shukla  1   2 , Chris Thomas  1 , Margo VanOeffelen  8 , Veronika Vonstein  8 , Andrew S Warren  3 , Fangfang Xia  1   2 , Dawen Xie  3 , Hyunseung Yoo  1   2 , Rick Stevens  6   13
Affiliations

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

James J Davis et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
Cumulative growth of public and private genomes in PATRIC.
Figure 2.
Figure 2.
User-initiated analysis jobs completed by the PATRIC bioinformatic services. The top plot shows the use of high-volume services. The bottom plot shows the usage of lower volume and new services. Note the difference in scale between the two plots.
Figure 3.
Figure 3.
A data analysis workflow in PATRIC using the Genome Alignment Service. (A) The website interface allows the selection of genomes; (B) visualization of the aligned genomic regions with any deletions, insertions or rearrangements; (C) zooming in on the alignment will show the genes on the forward and reverse stands, which can be selected; (D) selecting a specific gene from the Genome Alignment viewer opens the PATRIC Feature Page, where all the data available for that gene are shown. (E) The Compare Region View tab on the PATRIC Gene Page shows conservation of the selected gene (shown in red), and also the surrounding genes. (F) Each gene is assigned to a genus-specific (PLFam) or global (PGFam) protein family that can be selected from the Feature Page, and the family members can be compared using the Multiple Sequence Alignment/Gene Tree tool.
See this image and copyright information in PMC

References

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