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Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29.

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

Author information

1
Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA rwattam@vbi.vt.edu.
2
Computation Institute, University of Chicago, Chicago, IL 60637, USA.
3
Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.
4
Department of Computer Science, University of Chicago, Chicago, IL 60637, USA.
5
Gydle Inc. 101-1332 Chanoine Morel Quebec, QC G1S, 4B4, Canada.
6
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
7
Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
8
Grado Department of Industrial & Systems Engineering, Virginia Tech, Blacksburg, VA 24060, USA.
9
Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA.
10
Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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.

PMID:
27899627
PMCID:
PMC5210524
DOI:
10.1093/nar/gkw1017
[Indexed for MEDLINE]
Free PMC Article

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