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PATRIC
PATRIC, the Pathosystems Resource Integration Center, provides integrated data and analysis tools to support biomedical research on bacterial infectious diseases.
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2020-04-28 11:33:44 UTC
annotation, genomics, genomes, metagenomics, metagenomes, genes, proteins, data capture, metabolic reconstruction, analysis tools, database, transcriptomics, data visualization, proteomics, phages

PATRIC

PATRIC provides integrated data and analysis tools to support biomedical research on bacterial infectious diseases. A variety of published genome, pathway, protein family and transcriptomics data can be analyzed and mined. Users can also upload their personal data for genomic, metagenomic, transcriptomic, proteomic and metabolomic analysis and comparison.
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Website

Notes from User

  • This platform is updated every 3 months with the new genomes from NCBI so quite up to date.
  • Great genome annoation tool from Fasta files to integrated genome in Patric in a few hours.
  • Genome amd feature groups are a great tool to keep track of data you need for your projects.
  • Many useful tools such as trees, proteome comparisons and pathway comparisons.
  • Extensive tutorials and help are available through the Help tab. {.is-info}

Citations

If you use PATRIC web resources to assist in research publications or proposals please cite

  • Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. PMID: 27899627. PMCID: PMC5210524. {.grid-list}

For annotations generated using the PATRIC RASTtk-enabled Genome Annotation Service, please cite

  • Brettin, T., J. J. Davis, T. Disz, R. A. Edwards, S. Gerdes, G. J. Olsen, R. Olson, R. Overbeek, B. Parrello, G. D. Pusch, M. Shukla, J. A. Thomason, 3rd, R. Stevens, V. Vonstein, A. R. Wattam and F. Xia. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015. 5: 8365. PMID: 25666585. PMCID: PMC4322359. {.grid-list}