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

Abstract

Here, the Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center. 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.

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID)
OSTI Identifier:
1373595
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 45; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Davis, James J., Brettin, Thomas, Dietrich, Emily M., Gerdes, Svetlana, Henry, Christopher S., Murphy-Olson, Daniel E., Olson, Robert, Parrello, Bruce D., Pusch, Gordon D., Shukla, Maulik P., Vonstein, Veronika, Xia, Fangfang, Yoo, Hyunseung, and Stevens, Rick L. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. United States: N. p., 2016. Web. doi:10.1093/nar/gkw1017.
Davis, James J., Brettin, Thomas, Dietrich, Emily M., Gerdes, Svetlana, Henry, Christopher S., Murphy-Olson, Daniel E., Olson, Robert, Parrello, Bruce D., Pusch, Gordon D., Shukla, Maulik P., Vonstein, Veronika, Xia, Fangfang, Yoo, Hyunseung, & Stevens, Rick L. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. United States. doi:10.1093/nar/gkw1017.
Davis, James J., Brettin, Thomas, Dietrich, Emily M., Gerdes, Svetlana, Henry, Christopher S., Murphy-Olson, Daniel E., Olson, Robert, Parrello, Bruce D., Pusch, Gordon D., Shukla, Maulik P., Vonstein, Veronika, Xia, Fangfang, Yoo, Hyunseung, and Stevens, Rick L. Mon . "Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center". United States. doi:10.1093/nar/gkw1017. https://www.osti.gov/servlets/purl/1373595.
@article{osti_1373595,
title = {Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center},
author = {Davis, James J. and Brettin, Thomas and Dietrich, Emily M. and Gerdes, Svetlana and Henry, Christopher S. and Murphy-Olson, Daniel E. and Olson, Robert and Parrello, Bruce D. and Pusch, Gordon D. and Shukla, Maulik P. and Vonstein, Veronika and Xia, Fangfang and Yoo, Hyunseung and Stevens, Rick L.},
abstractNote = {Here, the Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center. 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.},
doi = {10.1093/nar/gkw1017},
journal = {Nucleic Acids Research},
issn = {0305-1048},
number = D1,
volume = 45,
place = {United States},
year = {2016},
month = {11}
}

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