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PATRIC, the bacterial bioinformatics database and analysis resource.

Alice R Wattam1, David Abraham, Oral Dalay

  • 1Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60637, USA, Grado Department of Industrial & Systems Engineering, Virginia Tech, Blacksburg, VA 24060, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, IL 60637, USA and Nestlé Institute of Health Sciences SA, Campus EPFL, Quartier de L'innovation, Lausanne, Switzerland.

Nucleic Acids Research
|November 15, 2013
PubMed
Summary

The Pathosystems Resource Integration Center (PATRIC) is a comprehensive bioinformatics resource for bacterial genomics and transcriptomics. It offers integrated data, analysis tools, and a private workspace for researchers studying bacterial pathogens.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Microbiology

Background:

  • The Pathosystems Resource Integration Center (PATRIC) is a key bioinformatics resource center for bacterial research.
  • It integrates diverse data types including genomics, transcriptomics, and protein-protein interactions.
  • PATRIC is funded by the National Institute of Allergy and Infectious Diseases.

Purpose of the Study:

  • To describe updates and enhancements to the PATRIC database.
  • To highlight the integration of various data types and analysis tools for bacterial research.
  • To provide researchers with a comprehensive resource for exploring bacterial pathogens.

Main Methods:

  • Integration of genomics, transcriptomics, protein-protein interaction, and structural data.
  • Consistent genome annotation using Rapid Annotations using Subsystems Technology (RAST).
  • Development of comparative genomic and transcriptomic analysis tools.

Main Results:

  • PATRIC now hosts over 10,000 bacterial genomes with consistent annotations.
  • The platform provides summarized data across taxonomic levels and for individual genes.
  • Includes integrated disease and protein-protein interaction information.

Conclusions:

  • PATRIC serves as a valuable, freely accessible online resource for the bacterial research community.
  • The integrated data and analysis tools facilitate comparative genomic and transcriptomic studies.
  • Updates enhance the utility of PATRIC for studying bacterial pathogens and their characteristics.