Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center

Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross OverbeekBruce Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo, Rick L. Stevens

Research output: Contribution to journalArticle

Abstract

The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by 'virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.

Original languageEnglish (US)
Pages (from-to)D535-D542
JournalNucleic acids research
Volume45
Issue numberD1
DOIs
StatePublished - Jan 1 2017

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Computational Biology
Research Personnel
Genome
Databases
RNA
Anti-Bacterial Agents

ASJC Scopus subject areas

  • Genetics

Cite this

Wattam, A. R., Davis, J. J., Assaf, R., Boisvert, S., Brettin, T., Bun, C., ... Stevens, R. L. (2017). Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic acids research, 45(D1), D535-D542. https://doi.org/10.1093/nar/gkw1017

Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. / Wattam, Alice R.; Davis, James J.; Assaf, Rida; Boisvert, Sébastien; Brettin, Thomas; Bun, Christopher; Conrad, Neal; Dietrich, Emily M.; Disz, Terry; Gabbard, Joseph L.; Gerdes, Svetlana; Henry, Christopher S.; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olsen, Gary J.; Murphy-Olson, Daniel E.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Warren, Andrew; Xia, Fangfang; Yoo, Hyunseung; Stevens, Rick L.

In: Nucleic acids research, Vol. 45, No. D1, 01.01.2017, p. D535-D542.

Research output: Contribution to journalArticle

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 2017, 'Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center', Nucleic acids research, vol. 45, no. D1, pp. D535-D542. https://doi.org/10.1093/nar/gkw1017
Wattam, Alice R. ; Davis, James J. ; Assaf, Rida ; Boisvert, Sébastien ; Brettin, Thomas ; Bun, Christopher ; Conrad, Neal ; Dietrich, Emily M. ; Disz, Terry ; Gabbard, Joseph L. ; Gerdes, Svetlana ; Henry, Christopher S. ; Kenyon, Ronald W. ; Machi, Dustin ; Mao, Chunhong ; Nordberg, Eric K. ; Olsen, Gary J. ; Murphy-Olson, Daniel E. ; Olson, Robert ; Overbeek, Ross ; Parrello, Bruce ; Pusch, Gordon D. ; Shukla, Maulik ; Vonstein, Veronika ; Warren, Andrew ; Xia, Fangfang ; Yoo, Hyunseung ; Stevens, Rick L. / Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. In: Nucleic acids research. 2017 ; Vol. 45, No. D1. pp. D535-D542.
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AU - Assaf, Rida

AU - Boisvert, Sébastien

AU - Brettin, Thomas

AU - Bun, Christopher

AU - Conrad, Neal

AU - Dietrich, Emily M.

AU - Disz, Terry

AU - Gabbard, Joseph L.

AU - Gerdes, Svetlana

AU - Henry, Christopher S.

AU - Kenyon, Ronald W.

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AU - Olsen, Gary J.

AU - Murphy-Olson, Daniel E.

AU - Olson, Robert

AU - Overbeek, Ross

AU - Parrello, Bruce

AU - Pusch, Gordon D.

AU - Shukla, Maulik

AU - Vonstein, Veronika

AU - Warren, Andrew

AU - Xia, Fangfang

AU - Yoo, Hyunseung

AU - Stevens, Rick L.

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