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

作者：Alice Rebecca Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas Scott Brettin, Christopher C Bun, Neal R. Conrad, Emily M. Dietrich, Terry L. 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 P. Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyunseung Yoo, Rick L. Stevens · 发表于：Nucleic Acids Research · 年份：2016 · DOI：10.1093/nar/gkw1017 · 被引用次数：1748 · 研究领域：Genomics and Phylogenetic Studies、Bacterial Identification and Susceptibility Testing、Gut microbiota and health

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.