- Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. [PMID: 27899627]
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 Overbeek, Bruce Parrello, Gordon D Pusch, Maulik Shukla, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo, Rick L Stevens
Nucleic acids research 2017:45(D1)
0 Citations (Google Scholar as of 2017-02-16)
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.
- PATRIC, the bacterial bioinformatics database and analysis resource. [PMID: 24225323]
Alice R Wattam, David Abraham, Oral Dalay, Terry L Disz, Timothy Driscoll, Joseph L Gabbard, Joseph J Gillespie, Roger Gough, Deborah Hix, Ronald Kenyon, Dustin Machi, Chunhong Mao, Eric K Nordberg, Robert Olson, Ross Overbeek, Gordon D Pusch, Maulik Shukla, Julie Schulman, Rick L Stevens, Daniel E Sullivan, Veronika Vonstein, Andrew Warren, Rebecca Will, Meredith J C Wilson, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Bruno W Sobral
Nucleic acids research 2014:42(Database issue)
279 Citations (Google Scholar as of 2017-02-16)
Abstract: The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.