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. 2023 Jan 6;51(D1):D678-D689.
doi: 10.1093/nar/gkac1003.

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

Robert D Olson  1   2 , Rida Assaf  3 , Thomas Brettin  1   4 , Neal Conrad  1   2 , Clark Cucinell  5 , James J Davis  1   2 , Donald M Dempsey  6 , Allan Dickerman  5 , Emily M Dietrich  1   2 , Ronald W Kenyon  5 , Mehmet Kuscuoglu  7 , Elliot J Lefkowitz  6 , Jian Lu  8 , Dustin Machi  5 , Catherine Macken  9 , Chunhong Mao  5 , Anna Niewiadomska  7 , Marcus Nguyen  1   2 , Gary J Olsen  10 , Jamie C Overbeek  1   2 , Bruce Parrello  1   11 , Victoria Parrello  11 , Jacob S Porter  4 , Gordon D Pusch  11 , Maulik Shukla  1   2 , Indresh Singh  8 , Lucy Stewart  7 , Gene Tan  7 , Chris Thomas  1   2 , Margo VanOeffelen  11 , Veronika Vonstein  11 , Zachary S Wallace  6   12 , Andrew S Warren  5 , Alice R Wattam  5 , Fangfang Xia  1   2 , Hyunseung Yoo  1   2 , Yun Zhang  7 , Christian M Zmasek  7 , Richard H Scheuermann  7   13   14   15 , Rick L Stevens  4   16
Affiliations

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

Robert D Olson et al. Nucleic Acids Res. .

Abstract

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

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Figures

Figure 1.
Figure 1.
Growth of genome sequences in the BRC resources. Dates prior to 2020 include separate data for IRD, ViPR and PATRIC; dates after 2020 include data from BV-BRC. The large jump in viral genomes in 2020 coincides with the SARS-CoV-2 pandemic. Private genomes represent sequences uploaded and analyzed by individual users.
Figure 2.
Figure 2.
The BV-BRC home page. Various ways for accessing bacterial and viral data are shown.
Figure 3.
Figure 3.
New and enhanced visual analytics tools at BV-BRC. Top left: the surveillance map viewer based on Google Maps, top right: the Archaeopteryx Tree Viewer for the Gene tree and Phylogenetic tree services, bottom left: the enhanced compare regions viewer, bottom right: The new protein structure viewer.
Figure 4.
Figure 4.
Overview of the SARS-CoV-2 Variant Tracker. The top left panel shows the landing page for the Delta variant of concern, the top right panel shows the prevalence of the D614G variant, the bottom left panel shows variant frequency by month in the USA, and the bottom right shows tracks that are available for viewing from the genome browser, which include open reading frames, active sites, antibody epitopes, and antibody binding escape data.
Figure 5.
Figure 5.
Cumulative growth in registered users for BV-BRC. For dates prior to 2020, data have been combined for PATRIC, IRD and ViPR.
Figure 6.
Figure 6.
Growth in user jobs and services. The bar chart shows the growth in jobs per year starting with the PATRIC services in 2015. Boxes show the approximate year in which each service was either developed or integrated.
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References

    1. Greene J.M., Collins F., Lefkowitz E.J., Roos D., Scheuermann R.H., Sobral B., Stevens R., White O., Di Francesco V.. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect. Immun. 2007; 75:3212–3219. - PMC - PubMed
    1. Amos B., Aurrecoechea C., Barba M., Barreto A., Basenko E.Y., Belnap R., Blevins A.S., Böhme U., Brestelli J., Brunk B.P.. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 2022; 50:D898–D911. - PMC - PubMed
    1. Davis J.J., Wattam A.R., Aziz R.K., Brettin T., Butler R., Butler R.M., Chlenski P., Conrad N., Dickerman A., Dietrich E.M.. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 2020; 48:D606–D612. - PMC - PubMed
    1. Zhang Y., Aevermann B.D., Anderson T.K., Burke D.F., Dauphin G., Gu Z., He S., Kumar S., Larsen C.N., Lee A.J.. Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res. 2017; 45:D466–D474. - PMC - PubMed
    1. Pickett B.E., Sadat E.L., Zhang Y., Noronha J.M., Squires R.B., Hunt V., Liu M., Kumar S., Zaremba S., Gu Z.. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 2012; 40:D593–D598. - PMC - PubMed

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