Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center - PubMed (original) (raw)

. 2017 Jan 4;45(D1):D535-D542.

doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29.

James J Davis 2 3, Rida Assaf 4, Sébastien Boisvert 5, Thomas Brettin 2 3, Christopher Bun 4, Neal Conrad 2 6, Emily M Dietrich 2 3, Terry Disz 7, Joseph L Gabbard 8, Svetlana Gerdes 7, Christopher S Henry 6, Ronald W Kenyon 9, Dustin Machi 9, Chunhong Mao 9, Eric K Nordberg 9, Gary J Olsen 10, Daniel E Murphy-Olson 3, Robert Olson 2 6, Ross Overbeek 3 7, Bruce Parrello 3 7, Gordon D Pusch 7, Maulik Shukla 2 3, Veronika Vonstein 7, Andrew Warren 9, Fangfang Xia 2 6, Hyunseung Yoo 2 3, Rick L Stevens 2 3 4

Affiliations

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

Alice R Wattam et al. Nucleic Acids Res. 2017.

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.

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

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Figures

Figure 1.

Figure 1.

New layout of the PATRIC homepage (

https://www.patricbrc.org

) with easy access to data, tools and the private user workspace.

Figure 2.

Figure 2.

The growth in the number of jobs submitted and processed by registered users at PATRIC since the new assembly, annotation, metabolic modeling, proteome comparison, expression import and RNA-Seq services were implemented in 2015. The variation service was a recent addition in May 2016.

Figure 3.

Figure 3.

The various assembly strategies now offered at PATRIC.

Figure 4.

Figure 4.

The number of genomes available in PATRIC have an almost exponential growth since the resource began in 2004.

Figure 5.

Figure 5.

Antimicrobial Resistance Data summaries are now available on organism landing pages at PATRIC. This example shows the current data available for Mycobacterium genomes.

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